Variant report

Variant	rs12023298
Chromosome Location	chr1:227729414-227729415
allele	A/C
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:227727749..227729472-chr1:227739111..227740675,2	K562	blood:
2	chr1:227721537..227724263-chr1:227727527..227730135,2	MCF-7	breast:
3	chr1:227725139..227726773-chr1:227727190..227729662,2	K562	blood:
4	chr1:227725436..227728346-chr1:227728933..227731230,4	MCF-7	breast:
5	chr1:227728970..227731707-chr1:227751101..227754291,3	MCF-7	breast:
6	chr1:227726703..227728573-chr1:227729012..227731358,2	K562	blood:
7	chr1:227729010..227735281-chr1:227748522..227752811,6	MCF-7	breast:
8	chr1:227727960..227729815-chr1:228131832..228133962,2	MCF-7	breast:
9	chr1:227728158..227729940-chr1:227914897..227917653,2	MCF-7	breast:
10	chr1:227728577..227730296-chr1:227730401..227732480,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000202264	Chromatin interaction
ENSG00000143740	Chromatin interaction
ENSG00000181450	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1021553	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1021554	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10495276	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10799423	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10799431	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10799432	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10799433	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10799434	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10799435	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10916158	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10916159	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10916165	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10916169	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10916175	0.91[EUR][1000 genomes]
rs10916176	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10916179	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10916182	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10916183	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10916184	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10916185	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10916187	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11484723	0.87[EUR][1000 genomes]
rs11580570	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12025815	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12040302	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12070002	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12070036	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12079123	0.91[EUR][1000 genomes]
rs12080321	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12132444	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12740317	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1407718	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1495842	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1495845	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1495847	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1845758	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2018401	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2088210	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2088211	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2088212	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2088214	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2093609	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2093610	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2132367	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2201571	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2644140	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28407112	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2935145	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2935146	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2935147	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2935152	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2935155	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2999741	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2999743	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2999744	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2999745	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2999746	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3010183	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3010186	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3010190	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3010191	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3010192	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3010193	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3010194	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3010195	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3010196	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4359006	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4653512	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4653514	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4653515	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4653848	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4653849	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4653850	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4653853	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6664682	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6671825	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6697867	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7512348	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7523915	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7528094	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7539914	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7542685	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7551459	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs903683	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs903684	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs903690	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs903697	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs951083	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs976959	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	esv2753828	chr1:227670265-227791265	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv873244	chr1:227682414-227736363	Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv873246	chr1:227694948-227884465	Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1007479	chr1:227695868-227984466	Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
6	nsv873247	chr1:227697381-227736363	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv873248	chr1:227710381-227786033	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv947520	chr1:227724042-227750192	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv947560	chr1:227726600-227750192	ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227726200-227729600	Weak transcription	Aorta	Aorta
2	chr1:227728400-227729600	Enhancers	Spleen	Spleen
3	chr1:227728800-227730400	Active TSS	Brain Anterior Caudate	brain
4	chr1:227729000-227729800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
5	chr1:227729000-227729800	Flanking Active TSS	Stomach Smooth Muscle	stomach
6	chr1:227729200-227729600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr1:227729200-227729600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
8	chr1:227729200-227729600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr1:227729200-227729600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr1:227729200-227729600	Flanking Active TSS	Brain Angular Gyrus	brain
11	chr1:227729200-227729600	Flanking Active TSS	Brain Hippocampus Middle	brain
12	chr1:227729200-227729600	Flanking Active TSS	Brain Substantia Nigra	brain
13	chr1:227729200-227729600	Flanking Active TSS	Duodenum Mucosa	Duodenum
14	chr1:227729200-227729600	Flanking Active TSS	Lung	lung
15	chr1:227729200-227729800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:227729200-227729800	Enhancers	Fetal Lung	lung
17	chr1:227729200-227729800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
18	chr1:227729200-227730000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
19	chr1:227729200-227730000	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr1:227729200-227730200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:227729200-227730400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:227729200-227730400	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr1:227729200-227730400	Active TSS	Colon Smooth Muscle	Colon
24	chr1:227729200-227730400	Active TSS	Fetal Brain Female	brain
25	chr1:227729200-227730400	Active TSS	Rectal Smooth Muscle	rectum
26	chr1:227729200-227730600	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr1:227729200-227731000	Active TSS	Colonic Mucosa	Colon
28	chr1:227729400-227729600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
29	chr1:227729400-227729600	Transcr. at gene 5' and 3'	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr1:227729400-227729600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
31	chr1:227729400-227729600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
32	chr1:227729400-227729600	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr1:227729400-227729600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:227729400-227729600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr1:227729400-227729600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
36	chr1:227729400-227729600	Enhancers	Primary B cells from peripheral blood	blood
37	chr1:227729400-227729600	Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr1:227729400-227729600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr1:227729400-227729600	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr1:227729400-227729600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr1:227729400-227729600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr1:227729400-227729600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:227729400-227729600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr1:227729400-227729600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr1:227729400-227729600	Enhancers	Esophagus	oesophagus
46	chr1:227729400-227729600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
47	chr1:227729400-227729600	Active TSS	HMEC	breast
48	chr1:227729400-227729600	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
49	chr1:227729400-227729800	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr1:227729400-227729800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

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