Variant report

Variant	rs7917676
Chromosome Location	chr10:6390107-6390108
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	NFATC1	chr10:6389914-6390481	GM12878	blood:	n/a	n/a
2	MTA3	chr10:6389399-6390676	GM12878	blood:	n/a	n/a
3	NFIC	chr10:6389401-6390575	GM12878	blood:	n/a	n/a
4	IKZF1	chr10:6389569-6390538	GM12878	blood:	n/a	n/a
5	PAX5	chr10:6389942-6390382	GM12878	blood:	n/a	n/a
6	BCLAF1	chr10:6389901-6390516	GM12878	blood:	n/a	n/a
7	RCOR1	chr10:6389553-6390525	GM12878	blood:	n/a	n/a
8	WRNIP1	chr10:6389378-6390418	GM12878	blood:	n/a	n/a
9	SPI1	chr10:6389940-6390501	HL-60	blood:	n/a	n/a
10	RUNX3	chr10:6389441-6390591	GM12878	blood:	n/a	n/a
11	EBF1	chr10:6389465-6390479	GM12878	blood:	n/a	n/a
12	RUNX3	chr10:6389439-6390695	GM12878	blood:	n/a	n/a
13	SPI1	chr10:6389939-6390426	GM12891	blood:	n/a	n/a
14	POLR2A	chr10:6389875-6390370	U87	brain:	n/a	n/a
15	RFX5	chr10:6389965-6390585	GM12878	blood:	n/a	n/a
16	ELF1	chr10:6389834-6390327	GM12878	blood:	n/a	n/a
17	ETS1	chr10:6389932-6390468	GM12878	blood:	n/a	n/a
18	CEBPB	chr10:6389875-6390626	GM12878	blood:	n/a	n/a
19	FOXM1	chr10:6389866-6390547	GM12878	blood:	n/a	n/a
20	ZNF384	chr10:6389522-6390523	GM12878	blood:	n/a	n/a
21	MAX	chr10:6389944-6390763	NB4	blood:	n/a	n/a
22	RAD21	chr10:6390047-6390456	GM12878	blood:	n/a	n/a
23	STAT5A	chr10:6389576-6390523	GM12878	blood:	n/a	chr10:6390096-6390103 chr10:6389644-6389652
24	TAF1	chr10:6389960-6390283	GM12878	blood:	n/a	n/a
25	MTA3	chr10:6389905-6390466	GM12878	blood:	n/a	n/a
26	PAX5	chr10:6389985-6390225	GM12892	blood:	n/a	n/a
27	PML	chr10:6390053-6390372	GM12878	blood:	n/a	n/a
28	POLR2A	chr10:6389833-6390647	GM12878	blood:	n/a	n/a
29	EBF1	chr10:6389526-6390423	GM12878	blood:	n/a	n/a
30	NFATC1	chr10:6389871-6390517	GM12878	blood:	n/a	n/a
31	SP1	chr10:6389908-6390492	GM12878	blood:	n/a	n/a
32	SP1	chr10:6389874-6390519	GM12878	blood:	n/a	chr10:6389890-6389897
33	ATF2	chr10:6389827-6390596	GM12878	blood:	n/a	n/a
34	EP300	chr10:6389516-6390682	GM12878	blood:	n/a	chr10:6389539-6389546 chr10:6390216-6390230
35	PAX5	chr10:6389798-6390617	GM12878	blood:	n/a	n/a
36	POLR2A	chr10:6389951-6390571	GM12891	blood:	n/a	n/a
37	POLR2A	chr10:6389890-6390578	GM12891	blood:	n/a	n/a
38	SPI1	chr10:6390004-6390506	GM12878	blood:	n/a	n/a
39	ATF2	chr10:6389814-6390562	GM12878	blood:	n/a	n/a
40	TCF3	chr10:6389929-6390415	GM12878	blood:	n/a	n/a
41	CEBPB	chr10:6390009-6390436	GM12878	blood:	n/a	n/a
42	BCLAF1	chr10:6389894-6390530	GM12878	blood:	n/a	n/a
43	TBL1XR1	chr10:6389557-6390699	GM12878	blood:	n/a	n/a
44	RELA	chr10:6389537-6390595	GM18505	blood:	n/a	n/a
45	FOXM1	chr10:6389420-6390588	GM12878	blood:	n/a	n/a
46	EBF1	chr10:6389499-6390497	GM12878	blood:	n/a	n/a
47	BCL11A	chr10:6389956-6390532	GM12878	blood:	n/a	n/a
48	STAT5A	chr10:6389930-6390439	GM12878	blood:	n/a	chr10:6390096-6390103
49	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
50	MAX	chr10:6389798-6390497	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:6388010..6391003-chr10:6392017..6395362,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000212743	TF binding region
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	0.92[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2387397	0.82[CHB][hapmap];0.93[YRI][hapmap]
rs947470	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs947471	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]
rs947472	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[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:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6357200-6397400	Weak transcription	Pancreas	Pancrea
2	chr10:6386000-6390200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr10:6388200-6391200	Flanking Active TSS	Dnd41	blood
4	chr10:6388600-6390400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr10:6388600-6390600	Enhancers	A549	lung
6	chr10:6388600-6390600	Enhancers	HSMMtube	muscle
7	chr10:6388600-6390800	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr10:6388800-6390600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr10:6388800-6390800	Enhancers	Fetal Thymus	thymus
10	chr10:6388800-6391600	Enhancers	Fetal Brain Male	brain
11	chr10:6389000-6390600	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr10:6389000-6391200	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr10:6389000-6392600	Enhancers	Primary hematopoietic stem cells	blood
14	chr10:6389200-6390200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
15	chr10:6389200-6390400	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr10:6389200-6390600	Flanking Active TSS	Primary T cells from cord blood	blood
17	chr10:6389200-6390600	Enhancers	Brain Angular Gyrus	brain
18	chr10:6389200-6390600	Enhancers	Brain Cingulate Gyrus	brain
19	chr10:6389200-6390600	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr10:6389200-6390800	Enhancers	Brain Substantia Nigra	brain
21	chr10:6389200-6391200	Enhancers	Fetal Brain Female	brain
22	chr10:6389400-6390200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
23	chr10:6389400-6390200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
24	chr10:6389400-6390200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
25	chr10:6389400-6390200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr10:6389400-6390200	Enhancers	HMEC	breast
27	chr10:6389400-6390200	Enhancers	NH-A	brain
28	chr10:6389400-6390400	Enhancers	Placenta	Placenta
29	chr10:6389400-6390400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
30	chr10:6389400-6390400	Enhancers	NHLF	lung
31	chr10:6389400-6390600	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr10:6389400-6390600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr10:6389400-6390600	Enhancers	Adipose Nuclei	Adipose
34	chr10:6389400-6390600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr10:6389400-6390600	Enhancers	Fetal Stomach	stomach
36	chr10:6389400-6390600	Flanking Active TSS	Thymus	Thymus
37	chr10:6389400-6391200	Flanking Active TSS	GM12878-XiMat	blood
38	chr10:6389600-6390200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr10:6389600-6390200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr10:6389600-6390400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr10:6389600-6390400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr10:6389600-6390400	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr10:6389600-6390400	Flanking Active TSS	NHDF-Ad	bronchial
44	chr10:6389600-6390600	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr10:6389600-6390600	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr10:6389600-6390600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr10:6389600-6390600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr10:6389600-6390800	Enhancers	Brain Germinal Matrix	brain
49	chr10:6389600-6390800	Enhancers	Fetal Lung	lung
50	chr10:6389600-6391000	Enhancers	ES-I3 Cell Line	embryonic stem cell

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