Variant report

Variant	rs6488162
Chromosome Location	chr12:33593127-33593128
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr12:33591697-33593128	MCF-7	breast:	n/a	chr12:33592813-33592823
2	RAD21	chr12:33592315-33593136	H1-hESC	embryonic stem cell:	n/a	chr12:33592669-33592683
3	UBTF	chr12:33591935-33593146	K562	blood:	n/a	n/a
4	BACH1	chr12:33592008-33593130	H1-hESC	embryonic stem cell:	n/a	n/a
5	E2F6	chr12:33591601-33593148	H1-hESC	embryonic stem cell:	n/a	chr12:33592531-33592542 chr12:33592698-33592710 chr12:33593087-33593096
6	SIN3AK20	chr12:33591550-33593253	MCF-7	breast:	n/a	n/a
7	E2F6	chr12:33591043-33593180	H1-hESC	embryonic stem cell:	n/a	chr12:33592531-33592542 chr12:33592698-33592710 chr12:33593087-33593096
8	POLR2A	chr12:33590894-33593146	MCF-7	breast:	n/a	n/a
9	HA-E2F1	chr12:33592220-33593298	MCF-7	breast:	n/a	chr12:33592531-33592542 chr12:33592698-33592710 chr12:33593087-33593096
10	CTBP2	chr12:33590950-33593166	H1-hESC	embryonic stem cell:	n/a	n/a
11	MAZ	chr12:33591828-33593400	K562	blood:	n/a	chr12:33592813-33592823
12	SUZ12	chr12:33591099-33593188	NT2-D1	testis:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:33593109..33594784-chr12:33753664..33755603,2	MCF-7	breast:
2	chr12:33592809..33594554-chr12:33758267..33760517,2	MCF-7	breast:

Variant related genes	Relation type
SYT10	TF binding region

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10506110	0.82[JPT][hapmap]
rs10732554	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10772076	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10844582	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10844611	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10844612	0.92[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10844613	0.84[CEU][hapmap];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10844614	0.85[CEU][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.81[ASN][1000 genomes]
rs11052705	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052736	0.84[ASN][1000 genomes]
rs12301124	0.83[CEU][hapmap];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12819439	0.84[ASN][1000 genomes]
rs12820541	0.81[ASN][1000 genomes]
rs1351682	0.89[ASW][hapmap];0.89[CEU][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1351683	0.92[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1447873	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1482987	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1482993	0.92[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1580396	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1601006	0.91[ASN][1000 genomes]
rs1601007	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1601008	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1842885	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1905240	0.84[ASN][1000 genomes]
rs1905408	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1905412	0.91[ASN][1000 genomes]
rs1905427	0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1994135	0.84[ASN][1000 genomes]
rs2389194	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2389218	0.89[ASN][1000 genomes]
rs2892701	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs4244865	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4244866	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4931717	0.81[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4931719	0.92[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7294492	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7311794	0.87[ASN][1000 genomes]
rs7315695	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7956576	1.00[YRI][hapmap]
rs7971226	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7980799	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9888363	0.81[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:31 , 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	nsv1035988	chr12:33399053-33699363	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv558248	chr12:33524082-33714866	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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
26	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
27	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
28	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
29	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
30	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
31	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

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:33589800-33595600	Active TSS	K562	blood
2	chr12:33590600-33593200	Active TSS	Brain Anterior Caudate	brain
3	chr12:33590600-33593400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
4	chr12:33591000-33593200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
5	chr12:33591000-33593200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
6	chr12:33591000-33593200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
7	chr12:33591000-33593200	Bivalent/Poised TSS	Fetal Kidney	kidney
8	chr12:33591000-33593400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
9	chr12:33591000-33593400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
10	chr12:33591200-33593200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
11	chr12:33591400-33593200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:33591400-33593200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:33591400-33593400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
14	chr12:33591400-33593400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr12:33591400-33593400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
16	chr12:33591600-33593400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
17	chr12:33591600-33593400	Bivalent/Poised TSS	Brain Germinal Matrix	brain
18	chr12:33591800-33593200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:33592000-33593200	Bivalent/Poised TSS	Fetal Brain Female	brain
20	chr12:33592000-33593200	Bivalent/Poised TSS	Fetal Stomach	stomach
21	chr12:33592000-33593200	Active TSS	Right Atrium	heart
22	chr12:33592000-33593200	Bivalent/Poised TSS	Small Intestine	intestine
23	chr12:33592000-33593400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:33592400-33593200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr12:33592400-33593400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr12:33592400-33593600	Active TSS	Rectal Smooth Muscle	rectum
27	chr12:33592600-33593200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
28	chr12:33592800-33593200	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr12:33592800-33593200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr12:33592800-33593200	Enhancers	Placenta	Placenta
31	chr12:33592800-33593200	Bivalent/Poised TSS	Right Ventricle	heart
32	chr12:33593000-33593200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr12:33593000-33593200	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
34	chr12:33593000-33593200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
35	chr12:33593000-33593200	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr12:33593000-33593200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr12:33593000-33593200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr12:33593000-33593200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr12:33593000-33593200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
40	chr12:33593000-33593200	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach

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