Variant report

Variant	rs947471
Chromosome Location	chr10:6389672-6389673
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	MTA3	chr10:6389399-6390676	GM12878	blood:	n/a	n/a
2	NFIC	chr10:6389401-6390575	GM12878	blood:	n/a	n/a
3	IKZF1	chr10:6389569-6390538	GM12878	blood:	n/a	n/a
4	RCOR1	chr10:6389553-6390525	GM12878	blood:	n/a	n/a
5	WRNIP1	chr10:6389378-6390418	GM12878	blood:	n/a	n/a
6	RUNX3	chr10:6389441-6390591	GM12878	blood:	n/a	n/a
7	EBF1	chr10:6389465-6390479	GM12878	blood:	n/a	n/a
8	RUNX3	chr10:6389439-6390695	GM12878	blood:	n/a	n/a
9	POLR2A	chr10:6389369-6389744	GM12892	blood:	n/a	n/a
10	BATF	chr10:6389506-6389791	GM12878	blood:	n/a	n/a
11	ZNF384	chr10:6389522-6390523	GM12878	blood:	n/a	n/a
12	STAT5A	chr10:6389576-6390523	GM12878	blood:	n/a	chr10:6390096-6390103 chr10:6389644-6389652
13	EBF1	chr10:6389526-6390423	GM12878	blood:	n/a	n/a
14	EP300	chr10:6389516-6390682	GM12878	blood:	n/a	chr10:6389539-6389546 chr10:6390216-6390230
15	MAX	chr10:6389324-6389709	NB4	blood:	n/a	n/a
16	TBL1XR1	chr10:6389557-6390699	GM12878	blood:	n/a	n/a
17	RELA	chr10:6389537-6390595	GM18505	blood:	n/a	n/a
18	FOXM1	chr10:6389420-6390588	GM12878	blood:	n/a	n/a
19	EBF1	chr10:6389499-6390497	GM12878	blood:	n/a	n/a
20	POU2F2	chr10:6389373-6390601	GM12878	blood:	n/a	chr10:6390162-6390177 chr10:6390164-6390176 chr10:6390162-6390176 chr10:6390165-6390174 chr10:6390165-6390175 chr10:6390165-6390175 chr10:6390166-6390173
21	POLR2A	chr10:6389240-6389785	U87	brain:	n/a	n/a
22	POLR2A	chr10:6389340-6390621	GM12878	blood:	n/a	n/a
23	RELA	chr10:6389526-6390556	GM10847	blood:	n/a	n/a
24	SMC3	chr10:6389442-6390600	GM12878	blood:	n/a	chr10:6390309-6390317
25	POLR2A	chr10:6389208-6391113	Raji	blood:	n/a	n/a
26	CHD2	chr10:6389501-6390832	GM12878	blood:	n/a	n/a
27	SPI1	chr10:6389441-6389751	GM12878	blood:	n/a	chr10:6389596-6389609
28	BHLHE40	chr10:6389474-6390671	GM12878	blood:	n/a	n/a
29	BATF	chr10:6389403-6389872	GM12878	blood:	n/a	n/a
30	RELA	chr10:6389558-6390615	GM19099	blood:	n/a	n/a
31	POLR2A	chr10:6389423-6389837	GM12878	blood:	n/a	n/a
32	ZEB1	chr10:6389602-6389908	GM12878	blood:	n/a	chr10:6389747-6389756 chr10:6389782-6389793
33	RELA	chr10:6389503-6390690	GM12891	blood:	n/a	n/a
34	STAT1	chr10:6389581-6389690	GM12878	blood:	n/a	chr10:6389644-6389652
35	CHD1	chr10:6389474-6390514	GM12878	blood:	n/a	n/a
36	RELA	chr10:6389515-6390596	GM18951	blood:	n/a	n/a
37	EP300	chr10:6389475-6390852	GM12878	blood:	n/a	chr10:6389539-6389546 chr10:6390216-6390230
38	STAT3	chr10:6389464-6390602	GM12878	blood:	n/a	chr10:6390096-6390103 chr10:6389644-6389652
39	NFIC	chr10:6389454-6390562	GM12878	blood:	n/a	n/a
40	POLR2A	chr10:6389236-6389805	GM12878	blood:	n/a	n/a
41	NFYB	chr10:6389459-6390443	GM12878	blood:	n/a	n/a
42	ELK1	chr10:6389539-6389739	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:6388010..6391003-chr10:6392017..6395362,3	MCF-7	breast:
2	chr10:6387353..6390083-chr10:6391651..6393610,2	K562	blood:
3	chr10:6335618..6337986-chr10:6387023..6389931,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000212743	TF binding region
ENSG00000226705	Chromatin interaction
ENSG00000212743	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11258213	1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2387397	0.82[CHB][hapmap]
rs7917676	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs947470	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs947472	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs947474	0.84[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1054044	chr10:6155144-6487217	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv894836	chr10:6246678-6435374	Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv430123	chr10:6309402-6448384	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv430125	chr10:6322167-6477267	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv1053440	chr10:6354798-6669469	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
7	nsv5676	chr10:6381200-6428950	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6357200-6397400	Weak transcription	Pancreas	Pancrea
2	chr10:6371600-6389800	Weak transcription	Aorta	Aorta
3	chr10:6386000-6390200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr10:6388200-6391200	Flanking Active TSS	Dnd41	blood
5	chr10:6388600-6390400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr10:6388600-6390600	Enhancers	A549	lung
7	chr10:6388600-6390600	Enhancers	HSMMtube	muscle
8	chr10:6388600-6390800	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr10:6388800-6390600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr10:6388800-6390800	Enhancers	Fetal Thymus	thymus
11	chr10:6388800-6391600	Enhancers	Fetal Brain Male	brain
12	chr10:6389000-6389800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr10:6389000-6390000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
14	chr10:6389000-6390600	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr10:6389000-6391200	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr10:6389000-6392600	Enhancers	Primary hematopoietic stem cells	blood
17	chr10:6389200-6390000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
18	chr10:6389200-6390000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
19	chr10:6389200-6390000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr10:6389200-6390000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
21	chr10:6389200-6390200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
22	chr10:6389200-6390400	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr10:6389200-6390600	Flanking Active TSS	Primary T cells from cord blood	blood
24	chr10:6389200-6390600	Enhancers	Brain Angular Gyrus	brain
25	chr10:6389200-6390600	Enhancers	Brain Cingulate Gyrus	brain
26	chr10:6389200-6390600	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr10:6389200-6390800	Enhancers	Brain Substantia Nigra	brain
28	chr10:6389200-6391200	Enhancers	Fetal Brain Female	brain
29	chr10:6389400-6389800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr10:6389400-6389800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr10:6389400-6389800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr10:6389400-6389800	Enhancers	Duodenum Mucosa	Duodenum
33	chr10:6389400-6390000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
34	chr10:6389400-6390000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
35	chr10:6389400-6390000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
36	chr10:6389400-6390000	Flanking Active TSS	Brain Hippocampus Middle	brain
37	chr10:6389400-6390000	Enhancers	Spleen	Spleen
38	chr10:6389400-6390000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
39	chr10:6389400-6390000	Flanking Active TSS	Osteobl	bone
40	chr10:6389400-6390200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
41	chr10:6389400-6390200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
42	chr10:6389400-6390200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
43	chr10:6389400-6390200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr10:6389400-6390200	Enhancers	HMEC	breast
45	chr10:6389400-6390200	Enhancers	NH-A	brain
46	chr10:6389400-6390400	Enhancers	Placenta	Placenta
47	chr10:6389400-6390400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr10:6389400-6390400	Enhancers	NHLF	lung
49	chr10:6389400-6390600	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr10:6389400-6390600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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