Variant report

Variant	rs7954275
Chromosome Location	chr12:31904510-31904511
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	NFIC	chr12:31904033-31904772	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr12:31903016-31905710	GM12878	blood:	n/a	n/a
3	GTF3C2	chr12:31904203-31904744	Hela-S3	cervix:	n/a	n/a
4	PAX5	chr12:31904467-31904966	GM12878	blood:	n/a	n/a
5	EP300	chr12:31903812-31904819	ECC-1	luminal epithelium:	n/a	n/a
6	ESRRA	chr12:31902945-31906220	GM12878	blood:	n/a	chr12:31905114-31905124 chr12:31905112-31905124 chr12:31905112-31905125 chr12:31905114-31905124
7	POLR2A	chr12:31904397-31904942	GM12878	blood:	n/a	n/a
8	FOS	chr12:31904492-31904659	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr12:31902962-31905703	GM12878	blood:	n/a	n/a
10	SPI1	chr12:31904488-31905223	GM12878	blood:	n/a	chr12:31904918-31904927 chr12:31904916-31904929
11	FOS	chr12:31904491-31904552	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:31900170..31902250-chr12:31904037..31906770,3	MCF-7	breast:
2	chr12:31902147..31904881-chr12:32110992..32113730,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223722	TF binding region
ENSG00000256843	TF binding region
ENSG00000174718	Chromatin interaction
ENSG00000256843	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11051556	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11051558	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11051560	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11051561	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11051562	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11051564	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11051565	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11611575	0.87[EUR][1000 genomes]
rs11613702	0.81[EUR][1000 genomes]
rs12320166	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34841509	0.85[EUR][1000 genomes]
rs36117515	0.88[EUR][1000 genomes]
rs4931552	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4931555	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7307184	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73090346	0.84[EUR][1000 genomes]
rs73090395	0.95[EUR][1000 genomes]
rs7312417	0.95[EUR][1000 genomes]
rs7954012	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7964078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7964389	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1043010	chr12:31798446-32143151	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv541446	chr12:31798446-32143151	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	esv3432694	chr12:31801467-32109828	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv898966	chr12:31810126-31944985	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	esv2422415	chr12:31863360-31930722	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv558100	chr12:31866833-32185924	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
8	nsv1045464	chr12:31869888-32183792	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	nsv541447	chr12:31869888-32183792	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
10	esv3363806	chr12:31872264-32410283	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
11	esv3508621	chr12:31872654-32410593	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
12	esv3508622	chr12:31872654-32410593	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
13	nsv558101	chr12:31876666-32006563	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
14	nsv1050448	chr12:31877289-31927006	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
15	nsv558102	chr12:31889824-31907409	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv975473	chr12:31895430-31908180	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv8940	chr12:31899904-31987363	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
18	nsv442261	chr12:31900550-31909906	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	esv2421936	chr12:31900550-31909908	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
20	esv2760910	chr12:31900550-31909908	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
21	nsv558103	chr12:31900550-31909908	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
22	nsv558104	chr12:31900550-31910908	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
23	nsv558105	chr12:31900550-31912588	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
24	nsv558106	chr12:31900550-31914143	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
25	nsv558107	chr12:31900550-31919188	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
26	esv1836353	chr12:31903771-31912588	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
27	esv1841335	chr12:31903771-31912588	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
28	nsv818904	chr12:31903771-31912588	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
29	nsv515490	chr12:31903771-31919188	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
30	esv11695	chr12:31904381-31911808	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31889400-31905800	Enhancers	Primary B cells from peripheral blood	blood
2	chr12:31893600-31905800	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr12:31899600-31905200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:31900000-31905200	Weak transcription	Primary T cells from cord blood	blood
5	chr12:31900000-31905800	Enhancers	Primary B cells from cord blood	blood
6	chr12:31900000-31906400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:31901000-31909800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr12:31901800-31905600	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr12:31901800-31905800	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr12:31902000-31904600	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr12:31902400-31905400	Weak transcription	Adipose Nuclei	Adipose
12	chr12:31902600-31904800	Enhancers	HUVEC	blood vessel
13	chr12:31902600-31905200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr12:31902600-31905200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr12:31902600-31905200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:31902600-31905200	Weak transcription	HSMMtube	muscle
17	chr12:31902600-31905400	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr12:31902600-31906400	Enhancers	Primary T cells fromperipheralblood	blood
19	chr12:31902600-31908600	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr12:31902600-31908600	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr12:31902600-31912800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr12:31903000-31904800	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr12:31903000-31904800	Enhancers	Dnd41	blood
24	chr12:31903200-31904600	Enhancers	NHEK	skin
25	chr12:31903200-31905600	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr12:31903200-31905600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr12:31903400-31904800	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr12:31903400-31905600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
29	chr12:31903400-31905600	Enhancers	Spleen	Spleen
30	chr12:31903600-31904800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr12:31903600-31905400	Enhancers	Placenta	Placenta
32	chr12:31903600-31912800	Weak transcription	Gastric	stomach
33	chr12:31903800-31904600	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr12:31903800-31905000	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr12:31903800-31905000	Enhancers	Monocytes-CD14+_RO01746	blood
36	chr12:31903800-31905200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr12:31903800-31905800	Weak transcription	Right Atrium	heart
38	chr12:31903800-31909800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr12:31904000-31904800	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr12:31904000-31905000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr12:31904000-31905400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr12:31904000-31905600	Enhancers	Primary neutrophils fromperipheralblood	blood
43	chr12:31904000-31909600	Weak transcription	HMEC	breast
44	chr12:31904200-31904600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr12:31904200-31904800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr12:31904200-31905000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr12:31904200-31905000	Weak transcription	Thymus	Thymus
48	chr12:31904200-31905200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr12:31904200-31908400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr12:31904200-31909600	Weak transcription	Hela-S3	cervix

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