Variant report

Variant	rs12828716
Chromosome Location	chr12:33740842-33740843
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:33590853..33594919-chr12:33737580..33741920,6	MCF-7	breast:
2	chr12:33589726..33596989-chr12:33737254..33743557,12	MCF-7	breast:
3	chr12:33738598..33741307-chr8:42697129..42698949,2	MCF-7	breast:
4	chr12:33734204..33736505-chr12:33740513..33742206,2	K562	blood:
5	chr12:33740467..33741676-chr12:33762290..33763074,5	MCF-7	breast:
6	chr12:33586288..33588588-chr12:33738098..33741571,3	MCF-7	breast:
7	chr12:33041897..33044565-chr12:33740312..33741870,2	K562	blood:
8	chr12:33673352..33675554-chr12:33738881..33741351,2	MCF-7	breast:
9	chr12:33740590..33741231-chr12:33762284..33763123,2	MCF-7	breast:
10	chr12:33700293..33703250-chr12:33739121..33741427,2	K562	blood:
11	chr12:32906746..32910896-chr12:33738987..33744699,5	MCF-7	breast:
12	chr12:33590760..33594067-chr12:33739942..33743332,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000139131	Chromatin interaction
ENSG00000131931	Chromatin interaction
ENSG00000110975	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10506110	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10743824	0.80[EUR][1000 genomes]
rs10743825	0.86[EUR][1000 genomes]
rs10743826	0.92[EUR][1000 genomes]
rs10772097	0.90[EUR][1000 genomes]
rs10772098	0.99[EUR][1000 genomes]
rs10772103	0.86[EUR][1000 genomes]
rs10772105	0.84[EUR][1000 genomes]
rs10772107	0.82[EUR][1000 genomes]
rs10844644	0.87[EUR][1000 genomes]
rs10844645	0.97[EUR][1000 genomes]
rs10844646	0.89[EUR][1000 genomes]
rs10844648	0.99[EUR][1000 genomes]
rs10844651	0.98[EUR][1000 genomes]
rs10844652	0.97[EUR][1000 genomes]
rs10844653	0.98[EUR][1000 genomes]
rs10844654	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844655	0.92[EUR][1000 genomes]
rs10844662	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844669	0.92[EUR][1000 genomes]
rs10844671	0.86[EUR][1000 genomes]
rs10844677	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10844678	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10844679	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11052768	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052813	0.86[EUR][1000 genomes]
rs11052815	0.82[EUR][1000 genomes]
rs11052819	0.82[EUR][1000 genomes]
rs11052820	0.87[EUR][1000 genomes]
rs11052823	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11052826	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11052829	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11052830	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11611987	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12146798	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12366322	0.87[EUR][1000 genomes]
rs12369424	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12369448	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12370711	0.85[EUR][1000 genomes]
rs12371062	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12818637	0.91[EUR][1000 genomes]
rs12820852	0.85[EUR][1000 genomes]
rs12823209	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12833526	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1384590	0.87[EUR][1000 genomes]
rs1384591	0.87[EUR][1000 genomes]
rs1386941	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1482994	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1873012	0.98[EUR][1000 genomes]
rs2200155	0.87[EUR][1000 genomes]
rs2218650	0.86[EUR][1000 genomes]
rs4459397	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs717712	0.93[EUR][1000 genomes]
rs7295852	0.85[EUR][1000 genomes]
rs7296424	0.84[EUR][1000 genomes]
rs7308214	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7312082	0.85[EUR][1000 genomes]
rs7312172	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7315881	0.84[EUR][1000 genomes]
rs7316878	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7962021	0.87[EUR][1000 genomes]
rs7968383	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:35 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037459	chr12:33310703-33905662	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv541459	chr12:33310703-33905662	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv558247	chr12:33481504-34245756	Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv1037735	chr12:33510115-34457196	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv469348	chr12:33524082-34245756	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv558249	chr12:33524082-34245756	Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv1047430	chr12:33526355-34435009	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
8	nsv1040037	chr12:33526355-34457196	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
9	nsv1055087	chr12:33527371-34078208	Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv541461	chr12:33527371-34078208	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	nsv1049273	chr12:33528203-34491300	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
12	nsv541462	chr12:33528203-34491300	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
13	nsv1042712	chr12:33528204-34427733	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
14	nsv541463	chr12:33528204-34427733	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
15	nsv1047392	chr12:33528403-34427593	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
16	nsv541464	chr12:33528403-34427593	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
17	nsv1051183	chr12:33528403-34491152	Active TSS Bivalent/Poised TSS ZNF genes & repeats Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
18	nsv541465	chr12:33528403-34491152	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
19	nsv1036239	chr12:33528828-34008814	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
20	nsv1037202	chr12:33538510-34064222	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
21	nsv541466	chr12:33538510-34064222	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
22	nsv1035385	chr12:33538510-34078208	Bivalent/Poised TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
23	nsv541467	chr12:33538510-34078208	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
24	nsv1052700	chr12:33542309-34078208	Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
25	nsv541468	chr12:33542309-34078208	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
26	nsv558255	chr12:33543220-34000986	Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
27	nsv1051117	chr12:33545148-34079849	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
28	nsv541469	chr12:33545148-34079849	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
29	nsv932193	chr12:33545149-34096639	Bivalent/Poised TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
30	nsv1052245	chr12:33606238-33766502	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
31	nsv1038731	chr12:33609560-33766502	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
32	nsv832369	chr12:33632228-33799741	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
33	nsv558256	chr12:33638795-33826241	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
34	nsv558257	chr12:33681398-33897481	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
35	nsv469739	chr12:33738564-33922234	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:33733200-33741400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:33738800-33743600	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr12:33739200-33743400	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr12:33739200-33743800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:33739200-33744400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:33739600-33741000	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr12:33739600-33741000	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr12:33739600-33741200	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr12:33739600-33742000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr12:33739600-33743600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:33739800-33741000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr12:33739800-33741400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr12:33739800-33743000	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr12:33739800-33743600	Enhancers	HMEC	breast
15	chr12:33740000-33741000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:33740000-33742000	Enhancers	HSMM	muscle
17	chr12:33740000-33742200	Enhancers	NH-A	brain
18	chr12:33740000-33743600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr12:33740200-33741000	Flanking Active TSS	K562	blood
20	chr12:33740200-33741600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr12:33740200-33742000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr12:33740400-33741000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr12:33740400-33741200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr12:33740400-33741400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr12:33740400-33741400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr12:33740400-33741400	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr12:33740600-33741000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:33740800-33741000	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr12:33740800-33741200	Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr12:33740800-33741400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr12:33740800-33741400	Enhancers	Fetal Intestine Large	intestine
32	chr12:33740800-33741400	Enhancers	NHEK	skin
33	chr12:33740800-33741600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
34	chr12:33740800-33742000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr12:33740800-33742000	Enhancers	Duodenum Mucosa	Duodenum
36	chr12:33740800-33742000	Flanking Active TSS	Hela-S3	cervix
37	chr12:33740800-33742000	Enhancers	HSMMtube	muscle

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