Variant report

Variant	rs10262457
Chromosome Location	chr7:149417460-149417461
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	NR2F2	chr7:149415570-149417593	K562	blood:	n/a	n/a
2	POLR2A	chr7:149415992-149417486	K562	blood:	n/a	n/a
3	CHD2	chr7:149416995-149418417	GM12878	blood:	n/a	n/a
4	HDAC2	chr7:149416787-149417491	K562	blood:	n/a	n/a
5	ZNF263	chr7:149416112-149418030	K562	blood:	n/a	chr7:149417247-149417268 chr7:149417308-149417329
6	EBF1	chr7:149416935-149418416	GM12878	blood:	n/a	chr7:149417657-149417670 chr7:149417657-149417668 chr7:149417659-149417668 chr7:149417658-149417668
7	STAT1	chr7:149417065-149417609	GM12878	blood:	n/a	n/a
8	ZNF263	chr7:149417005-149417717	HEK293-T-REx	kidney:	n/a	chr7:149417247-149417268 chr7:149417308-149417329
9	EBF1	chr7:149417454-149417943	GM12878	blood:	n/a	chr7:149417657-149417670 chr7:149417657-149417668 chr7:149417659-149417668 chr7:149417658-149417668
10	POLR2A	chr7:149415881-149417807	K562	blood:	n/a	n/a
11	MBD4	chr7:149417250-149417629	HepG2	liver:	n/a	n/a
12	MAFK	chr7:149417025-149417630	K562	blood:	n/a	n/a
13	E2F6	chr7:149416045-149417668	K562	blood:	n/a	n/a
14	EP300	chr7:149416823-149418059	GM12878	blood:	n/a	chr7:149417886-149417902
15	UBTF	chr7:149415933-149417579	K562	blood:	n/a	n/a
16	HMGN3	chr7:149416035-149417651	K562	blood:	n/a	n/a
17	RCOR1	chr7:149416032-149417512	K562	blood:	n/a	n/a
18	TAL1	chr7:149415961-149417606	K562	blood:	n/a	chr7:149415996-149416004
19	RELA	chr7:149417020-149417816	GM19193	blood:	n/a	n/a
20	SMARCB1	chr7:149415999-149417725	K562	blood:	n/a	n/a
21	ZNF143	chr7:149417075-149417888	GM12878	blood:	n/a	n/a
22	RCOR1	chr7:149417206-149417926	GM12878	blood:	n/a	n/a
23	SMARCA4	chr7:149415962-149417669	K562	blood:	n/a	n/a
24	POLR2A	chr7:149416973-149417668	K562	blood:	n/a	n/a
25	CBX3	chr7:149415539-149417509	K562	blood:	n/a	n/a
26	JUND	chr7:149415891-149417501	K562	blood:	n/a	chr7:149416325-149416336
27	ELK1	chr7:149417354-149417499	K562	blood:	n/a	n/a
28	UBTF	chr7:149417134-149417480	K562	blood:	n/a	n/a
29	RELA	chr7:149417001-149417897	GM18951	blood:	n/a	n/a
30	SMC3	chr7:149417417-149417518	GM12878	blood:	n/a	n/a
31	JUN	chr7:149415850-149417585	K562	blood:	n/a	chr7:149416366-149416379
32	MAX	chr7:149416041-149417678	K562	blood:	n/a	n/a
33	RCOR1	chr7:149416007-149417481	K562	blood:	n/a	n/a
34	BHLHE40	chr7:149417032-149418330	GM12878	blood:	n/a	chr7:149418189-149418205
35	RFX5	chr7:149417300-149418367	SK-N-SH	brain:	n/a	n/a
36	POLR2A	chr7:149416036-149417912	K562	blood:	n/a	n/a
37	TEAD4	chr7:149415791-149417610	K562	blood:	n/a	n/a
38	JUN	chr7:149417042-149417467	K562	blood:	n/a	n/a
39	MYC	chr7:149415909-149417497	K562	blood:	n/a	n/a
40	EBF1	chr7:149417426-149417968	GM12878	blood:	n/a	chr7:149417657-149417670 chr7:149417657-149417668 chr7:149417659-149417668 chr7:149417658-149417668
41	MAZ	chr7:149417445-149417791	HepG2	liver:	n/a	n/a
42	MAZ	chr7:149416048-149417845	K562	blood:	n/a	n/a
43	MXI1	chr7:149417062-149417945	GM12878	blood:	n/a	n/a
44	RELA	chr7:149416992-149417915	GM19099	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:149319991..149321797-chr7:149416838..149419034,2	MCF-7	breast:
2	chr7:149415554..149419677-chr7:149423548..149428331,6	K562	blood:

Variant related genes	Relation type
KRBA1	TF binding region
ENSG00000133619	Chromatin interaction
ENSG00000133624	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10231875	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10240931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10256826	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10256935	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10258658	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10952835	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11979707	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12666315	0.96[GIH][hapmap]
rs12670882	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17171280	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs28647767	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55727837	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56226490	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56265968	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60047316	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60647533	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66588543	0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67491931	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67647638	0.92[EUR][1000 genomes]
rs67657627	0.92[EUR][1000 genomes]
rs68129719	0.94[EUR][1000 genomes]
rs68139633	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6974082	0.96[GIH][hapmap]
rs73479712	0.94[EUR][1000 genomes]
rs7791608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7804205	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7808442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs867152	0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs885651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs885652	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.97[TSI][hapmap];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs885653	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[TSI][hapmap];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021849	chr7:149230929-149422239	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv1034350	chr7:149264094-149666356	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv539190	chr7:149264094-149666356	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1023901	chr7:149364044-149747442	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv539191	chr7:149364044-149747442	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv469576	chr7:149379626-149563233	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers 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 target site	21 gene(s)	inside rSNPs	diseases
7	nsv1031581	chr7:149386249-149570178	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv539192	chr7:149386249-149570178	Genic enhancers Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv465199	chr7:149398065-149462621	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv608979	chr7:149398065-149462621	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10262457	ABCF2	cis	parietal	SCAN
rs10262457	ZNF862	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:149412800-149418000	Weak transcription	Aorta	Aorta
2	chr7:149412800-149418600	Weak transcription	Primary B cells from cord blood	blood
3	chr7:149412800-149421400	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr7:149412800-149438800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr7:149413000-149418000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr7:149413000-149418000	Weak transcription	Small Intestine	intestine
7	chr7:149413000-149418200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr7:149413000-149418200	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr7:149413000-149424000	Weak transcription	Fetal Kidney	kidney
10	chr7:149413000-149433200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr7:149413200-149417800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr7:149413200-149417800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr7:149413200-149418000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr7:149413200-149418000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr7:149413200-149418400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr7:149413200-149421800	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr7:149413200-149426200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr7:149413200-149432000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr7:149413200-149433600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr7:149413400-149417600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr7:149413400-149417800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr7:149413400-149417800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr7:149413400-149418000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr7:149413400-149418200	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr7:149413400-149418200	Weak transcription	Fetal Thymus	thymus
26	chr7:149413400-149418400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr7:149413400-149418600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr7:149413400-149419200	Weak transcription	Primary B cells from peripheral blood	blood
29	chr7:149413400-149423000	Weak transcription	Colonic Mucosa	Colon
30	chr7:149413400-149424600	Weak transcription	HUVEC	blood vessel
31	chr7:149413400-149433400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr7:149413600-149418000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr7:149413800-149418000	Weak transcription	Fetal Lung	lung
34	chr7:149413800-149419800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr7:149414000-149417600	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr7:149414000-149430200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr7:149414600-149418400	Enhancers	Fetal Heart	heart
38	chr7:149414800-149438800	Weak transcription	Fetal Brain Male	brain
39	chr7:149415800-149418200	Enhancers	Left Ventricle	heart
40	chr7:149415800-149421800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr7:149416000-149417600	Genic enhancers	HUES6 Cell Line	embryonic stem cell
42	chr7:149416000-149417600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr7:149416000-149417600	Genic enhancers	Fetal Stomach	stomach
44	chr7:149416000-149417600	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr7:149416000-149417600	Enhancers	GM12878-XiMat	blood
46	chr7:149416000-149417600	Enhancers	NH-A	brain
47	chr7:149416000-149417800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr7:149416000-149417800	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr7:149416000-149417800	Enhancers	Colon Smooth Muscle	Colon
50	chr7:149416000-149417800	Enhancers	NHLF	lung

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