Variant report

Variant	rs2401386
Chromosome Location	chr12:9800058-9800059
allele	A/G
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	EP300	chr12:9799685-9800070	K562	blood:	n/a	n/a
2	GABPA	chr12:9800034-9801209	A549	lung:	n/a	n/a
3	UBTF	chr12:9800050-9801395	K562	blood:	n/a	n/a
4	TBL1XR1	chr12:9799984-9802966	GM12878	blood:	n/a	n/a
5	POLR2A	chr12:9799637-9800225	SK-N-MC	brain:	n/a	n/a
6	POLR2A	chr12:9799451-9804403	GM19193	blood:	n/a	n/a
7	RUNX3	chr12:9799672-9801651	GM12878	blood:	n/a	chr12:9800805-9800822
8	MTA3	chr12:9799406-9804477	GM12878	blood:	n/a	n/a
9	RUNX3	chr12:9799645-9802568	GM12878	blood:	n/a	chr12:9800805-9800822
10	TEAD4	chr12:9799580-9800076	K562	blood:	n/a	n/a
11	POLR2A	chr12:9799501-9804451	GM12891	blood:	n/a	n/a
12	IRF1	chr12:9799891-9802485	K562	blood:	n/a	chr12:9801699-9801712 chr12:9802381-9802392 chr12:9801697-9801711 chr12:9802380-9802394 chr12:9800630-9800644 chr12:9801698-9801711 chr12:9801737-9801744 chr12:9801701-9801712 chr12:9801702-9801712 chr12:9801699-9801713 chr12:9801700-9801714 chr12:9801698-9801712 chr12:9801699-9801713
13	KAP1	chr12:9799906-9802085	U2OS	brain:	n/a	chr12:9800521-9800529
14	POLR2A	chr12:9799408-9804409	GM19099	blood:	n/a	n/a
15	POLR2A	chr12:9799796-9802695	HepG2	liver:	n/a	n/a
16	MAZ	chr12:9799597-9801421	K562	blood:	n/a	n/a
17	CEBPD	chr12:9799700-9800109	K562	blood:	n/a	n/a
18	POLR2A	chr12:9799794-9802049	IMR90	lung:	n/a	n/a
19	KAP1	chr12:9799923-9802306	HEK293	kidney:	n/a	chr12:9800521-9800529
20	POLR2A	chr12:9799328-9804610	GM12878	blood:	n/a	n/a
21	POLR2A	chr12:9799314-9804469	GM12892	blood:	n/a	n/a
22	POLR2A	chr12:9799782-9803691	NB4	blood:	n/a	n/a
23	MAZ	chr12:9799286-9801365	IMR90	lung:	n/a	n/a
24	NFIC	chr12:9799779-9804349	GM12878	blood:	n/a	n/a
25	TBP	chr12:9799933-9800151	K562	blood:	n/a	n/a
26	FOSL2	chr12:9800026-9800511	A549	lung:	n/a	n/a
27	POLR2A	chr12:9799501-9804422	GM18526	blood:	n/a	n/a
28	STAT5A	chr12:9799903-9804021	GM12878	blood:	n/a	chr12:9800489-9800496 chr12:9801700-9801711 chr12:9803497-9803505 chr12:9800768-9800780
29	POLR2A	chr12:9799475-9804347	GM12892	blood:	n/a	n/a
30	POLR2A	chr12:9799681-9804387	Raji	blood:	n/a	n/a
31	SMARCB1	chr12:9799935-9801265	Hela-S3	cervix:	n/a	n/a
32	RELA	chr12:9799625-9804451	GM19193	blood:	n/a	n/a
33	RELA	chr12:9799837-9804323	GM18505	blood:	n/a	n/a
34	ZNF263	chr12:9799773-9801418	HEK293-T-REx	kidney:	n/a	n/a
35	MEF2A	chr12:9800044-9801994	GM12878	blood:	n/a	n/a
36	STAT1	chr12:9799897-9800080	GM12878	blood:	n/a	n/a
37	BCLAF1	chr12:9799795-9803076	GM12878	blood:	n/a	chr12:9800683-9800696 chr12:9800565-9800578
38	POLR2A	chr12:9799830-9801435	K562	blood:	n/a	n/a
39	RELA	chr12:9799841-9804488	GM18951	blood:	n/a	n/a
40	POLR2A	chr12:9799734-9803978	MCF10A-Er-Src	breast:	n/a	n/a
41	POLR2A	chr12:9799520-9804579	GM12878	blood:	n/a	n/a
42	TAL1	chr12:9799641-9800075	K562	blood:	n/a	n/a
43	JUND	chr12:9799933-9801704	K562	blood:	n/a	chr12:9800672-9800681
44	POLR2A	chr12:9794253-9800349	K562	blood:	n/a	n/a
45	POLR2A	chr12:9799517-9804360	GM12878	blood:	n/a	n/a
46	POLR2A	chr12:9799424-9801754	GM12892	blood:	n/a	n/a
47	POLR2A	chr12:9799348-9804458	GM12892	blood:	n/a	n/a
48	POLR2A	chr12:9799621-9801563	K562	blood:	n/a	n/a
49	POLR2A	chr12:9799786-9800072	MCF-7	breast:	n/a	n/a
50	POLR2A	chr12:9799943-9804384	GM15510	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:9799292..9802850-chr12:9823422..9827161,3	MCF-7	breast:
2	chr12:9799323..9802837-chr12:9803671..9808302,9	K562	blood:
3	chr12:9786143..9793024-chr12:9797652..9803573,13	MCF-7	breast:
4	chr12:9522809..9525392-chr12:9798242..9800347,2	K562	blood:
5	chr12:9794237..9796835-chr12:9798704..9800341,2	MCF-7	breast:
6	chr12:9799537..9802341-chr12:9814175..9817797,3	K562	blood:
7	chr12:9798786..9803516-chr12:9803864..9807970,10	MCF-7	breast:
8	chr12:9785588..9787603-chr12:9798282..9800898,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000256594	TF binding region
ENSG00000272917	Chromatin interaction
ENSG00000256594	Chromatin interaction
ENSG00000069493	Chromatin interaction
ENSG00000233719	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10047657	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs10743789	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10743806	0.83[EUR][1000 genomes]
rs10771927	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs10771929	0.83[ASN][1000 genomes]
rs10771930	0.83[ASN][1000 genomes]
rs10771947	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10772001	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs10844160	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10844161	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10844206	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10844225	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10844233	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10844269	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10844325	0.83[EUR][1000 genomes]
rs10844373	0.83[EUR][1000 genomes]
rs11051877	0.80[ASN][1000 genomes]
rs11051879	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11052008	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11052013	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs11052027	0.82[ASN][1000 genomes]
rs11052031	0.83[ASN][1000 genomes]
rs12301481	0.81[ASN][1000 genomes]
rs12308360	0.87[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1529418	0.84[ASN][1000 genomes]
rs1529419	0.81[ASN][1000 genomes]
rs1863873	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs1863874	0.83[EUR][1000 genomes]
rs1987426	0.81[ASN][1000 genomes]
rs2401385	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs34383380	0.83[EUR][1000 genomes]
rs35721310	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3764023	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4763715	0.89[ASN][1000 genomes]
rs4763716	0.91[ASN][1000 genomes]
rs4763717	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs5023032	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs66927586	0.81[ASN][1000 genomes]
rs7132715	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7138619	0.82[ASN][1000 genomes]
rs72656629	0.88[ASN][1000 genomes]
rs7302081	0.80[ASN][1000 genomes]
rs7310367	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7313927	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7314188	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7954289	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
4	esv1821732	chr12:9560087-9830668	Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv1823760	chr12:9560087-9830668	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv428271	chr12:9560087-9830668	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	esv2757489	chr12:9583455-9810764	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv917178	chr12:9637315-9820153	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9792800-9800200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:9794400-9800200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:9795800-9800200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:9796600-9800200	Weak transcription	Gastric	stomach
5	chr12:9798800-9800200	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr12:9798800-9800200	Enhancers	HUVEC	blood vessel
7	chr12:9799400-9800200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:9799400-9800200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:9799400-9800200	Enhancers	Placenta Amnion	Placenta Amnion
10	chr12:9799400-9800400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
11	chr12:9799400-9800600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
12	chr12:9799400-9800600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:9799400-9800600	Flanking Active TSS	GM12878-XiMat	blood
14	chr12:9799600-9800200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:9799600-9800200	Flanking Active TSS	Primary T cells from cord blood	blood
16	chr12:9799600-9800200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr12:9799600-9800200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr12:9799600-9800200	Enhancers	NHLF	lung
19	chr12:9799600-9800400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
20	chr12:9799600-9800600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
21	chr12:9799600-9800600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
22	chr12:9799600-9800600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
23	chr12:9799800-9800200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr12:9799800-9800200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr12:9799800-9800200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr12:9799800-9800200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr12:9799800-9800200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr12:9799800-9800200	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr12:9799800-9800200	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr12:9799800-9800200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr12:9799800-9800200	Enhancers	Brain Substantia Nigra	brain
32	chr12:9799800-9800200	Enhancers	Pancreas	Pancrea
33	chr12:9799800-9800200	Enhancers	Stomach Mucosa	stomach
34	chr12:9799800-9800200	Flanking Active TSS	A549	lung
35	chr12:9799800-9800200	Enhancers	Dnd41	blood
36	chr12:9799800-9800200	Enhancers	HMEC	breast
37	chr12:9799800-9800200	Enhancers	NHDF-Ad	bronchial
38	chr12:9799800-9800400	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr12:9799800-9800400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr12:9799800-9800400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr12:9799800-9800400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr12:9799800-9800400	Flanking Active TSS	Fetal Lung	lung
43	chr12:9799800-9800600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:9799800-9800800	Flanking Active TSS	Primary B cells from cord blood	blood
45	chr12:9799800-9800800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
46	chr12:9799800-9801400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr12:9799800-9801800	Active TSS	HUES48 Cell Line	embryonic stem cell
48	chr12:9799800-9802200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
49	chr12:9799800-9803600	Flanking Active TSS	Primary hematopoietic stem cells	blood
50	chr12:9800000-9800200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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