Variant report

Variant	rs10262131
Chromosome Location	chr7:39605313-39605314
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	USF2	chr7:39605250-39605450	Hela-S3	cervix:	n/a	chr7:39605259-39605270
2	FOXA1	chr7:39605119-39605530	HepG2	liver:	n/a	chr7:39605399-39605414 chr7:39605365-39605380
3	POLR2A	chr7:39605312-39606334	NB4	blood:	n/a	n/a
4	FOXA1	chr7:39605254-39605482	T-47D	breast:	n/a	chr7:39605399-39605414 chr7:39605365-39605380
5	PML	chr7:39605304-39606460	K562	blood:	n/a	n/a
6	FOXA1	chr7:39605117-39605534	T-47D	breast:	n/a	chr7:39605399-39605414 chr7:39605365-39605380
7	POLR2A	chr7:39605039-39606825	MCF10A-Er-Src	breast:	n/a	n/a
8	FOXA2	chr7:39605046-39605888	HepG2	liver:	n/a	n/a
9	HCFC1	chr7:39605177-39606969	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr7:39605178-39606441	MCF10A-Er-Src	breast:	n/a	n/a
11	GABPA	chr7:39605226-39606693	A549	lung:	n/a	n/a
12	POLR2A	chr7:39605175-39606534	GM12878	blood:	n/a	n/a
13	KAP1	chr7:39605272-39606201	U2OS	brain:	n/a	n/a
14	USF1	chr7:39605092-39605328	H1-hESC	embryonic stem cell:	n/a	n/a
15	FOXA2	chr7:39605246-39605543	A549	lung:	n/a	n/a
16	MXI1	chr7:39605191-39606518	IMR90	lung:	n/a	n/a
17	GABPA	chr7:39605290-39606678	SK-N-SH	brain:	n/a	n/a
18	FOXA2	chr7:39605272-39605614	A549	lung:	n/a	n/a
19	SIN3A	chr7:39605265-39606618	H1-hESC	embryonic stem cell:	n/a	n/a
20	MXI1	chr7:39604938-39607300	SK-N-SH	brain:	n/a	n/a
21	TBP	chr7:39605210-39606397	K562	blood:	n/a	n/a
22	CEBPB	chr7:39605220-39606506	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr7:39605177-39606615	PBDE	blood:	n/a	n/a
24	CUX1	chr7:39605174-39606010	K562	blood:	n/a	n/a
25	FOS	chr7:39605150-39605438	MCF10A-Er-Src	breast:	n/a	chr7:39605266-39605273 chr7:39605266-39605274 chr7:39605265-39605275
26	EP300	chr7:39605053-39605382	GM12878	blood:	n/a	chr7:39605266-39605275
27	POLR2A	chr7:39605226-39606473	K562	blood:	n/a	n/a
28	POLR2A	chr7:39605280-39606555	HepG2	liver:	n/a	n/a
29	MYC	chr7:39605311-39606342	K562	blood:	n/a	n/a
30	POLR2A	chr7:39605084-39606484	K562	blood:	n/a	n/a
31	FOXA1	chr7:39605094-39605518	HepG2	liver:	n/a	chr7:39605399-39605414 chr7:39605365-39605380
32	FOXA2	chr7:39605164-39605551	HepG2	liver:	n/a	n/a
33	CTCF	chr7:39605221-39606086	K562	blood:	n/a	n/a
34	MTA3	chr7:39605214-39606411	GM12878	blood:	n/a	n/a
35	POLR2A	chr7:39605283-39606574	HepG2	liver:	n/a	n/a
36	POLR2A	chr7:39605185-39606480	GM12891	blood:	n/a	n/a
37	POLR2A	chr7:39605076-39606454	SK-N-MC	brain:	n/a	n/a
38	HCFC1	chr7:39605287-39606384	K562	blood:	n/a	n/a
39	BHLHE40	chr7:39605270-39606262	GM12878	blood:	n/a	n/a
40	BHLHE40	chr7:39605211-39606254	K562	blood:	n/a	n/a
41	FOS	chr7:39605159-39605505	MCF10A-Er-Src	breast:	n/a	chr7:39605266-39605273 chr7:39605266-39605274 chr7:39605265-39605275
42	POLR2A	chr7:39605228-39606448	K562	blood:	n/a	n/a
43	FOXA1	chr7:39605055-39605687	HepG2	liver:	n/a	chr7:39605399-39605414 chr7:39605365-39605380
44	JUND	chr7:39605173-39606331	K562	blood:	n/a	chr7:39605266-39605273 chr7:39605266-39605274 chr7:39605265-39605275
45	FOXA1	chr7:39605075-39605640	HepG2	liver:	n/a	chr7:39605399-39605414 chr7:39605365-39605380
46	IRF1	chr7:39605309-39606317	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:39604710..39608797-chr7:39663149..39665225,4	K562	blood:
2	chr7:39603623..39606050-chr7:39662280..39665105,2	MCF-7	breast:
3	chr7:39605012..39607338-chr7:39986740..39989686,2	K562	blood:

Variant related genes	Relation type
YAE1D1	TF binding region
ENSG00000006451	Chromatin interaction
ENSG00000065883	Chromatin interaction
ENSG00000259826	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10232859	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10486799	1.00[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs1051162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11981810	0.97[ASN][1000 genomes]
rs17171592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17171599	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17171601	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17713701	0.94[ASN][1000 genomes]
rs17714026	0.90[ASN][1000 genomes]
rs17714061	1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs17770744	0.90[ASN][1000 genomes]
rs2288744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2876861	0.90[ASN][1000 genomes]
rs2971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35586222	0.99[ASN][1000 genomes]
rs59818431	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60942815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6947660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6973403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6978059	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73375667	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73375677	0.97[AFR][1000 genomes]
rs73375682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73375684	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73375686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7790984	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021180	chr7:39424988-39642261	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1026951	chr7:39429036-39642261	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1018430	chr7:39455497-39643569	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv887970	chr7:39587912-39688152	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39604200-39605600	Weak transcription	Small Intestine	intestine
2	chr7:39604600-39606600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr7:39605000-39605400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr7:39605000-39605400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr7:39605000-39605400	Enhancers	Primary B cells from peripheral blood	blood
6	chr7:39605000-39605400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
7	chr7:39605000-39605400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr7:39605000-39605400	Flanking Active TSS	Fetal Brain Female	brain
9	chr7:39605000-39605400	Flanking Active TSS	Hela-S3	cervix
10	chr7:39605000-39605400	Flanking Active TSS	NHEK	skin
11	chr7:39605000-39605400	Flanking Active TSS	Osteobl	bone
12	chr7:39605000-39605600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr7:39605000-39605600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr7:39605000-39605600	Flanking Active TSS	Dnd41	blood
15	chr7:39605000-39605800	Flanking Active TSS	Primary hematopoietic stem cells	blood
16	chr7:39605000-39605800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
17	chr7:39605000-39605800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr7:39605000-39606600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr7:39605000-39606600	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr7:39605000-39606800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr7:39605000-39606800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr7:39605000-39606800	Active TSS	Aorta	Aorta
23	chr7:39605000-39606800	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr7:39605000-39606800	Active TSS	GM12878-XiMat	blood
25	chr7:39605000-39606800	Active TSS	HMEC	breast
26	chr7:39605000-39606800	Active TSS	K562	blood
27	chr7:39605000-39607000	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr7:39605000-39607000	Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr7:39605000-39607000	Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr7:39605000-39607000	Active TSS	Fetal Kidney	kidney
31	chr7:39605000-39607000	Active TSS	NHDF-Ad	bronchial
32	chr7:39605000-39607200	Active TSS	HUES6 Cell Line	embryonic stem cell
33	chr7:39605000-39607200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr7:39605000-39607200	Active TSS	Rectal Smooth Muscle	rectum
35	chr7:39605000-39607400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr7:39605000-39607600	Active TSS	HUES48 Cell Line	embryonic stem cell
37	chr7:39605000-39607600	Active TSS	HUES64 Cell Line	embryonic stem cell
38	chr7:39605000-39607600	Active TSS	A549	lung
39	chr7:39605000-39607600	Active TSS	NHLF	lung
40	chr7:39605200-39605400	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr7:39605200-39605400	Flanking Active TSS	H9 Cell Line	embryonic stem cell
42	chr7:39605200-39605400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr7:39605200-39605400	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr7:39605200-39605400	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr7:39605200-39605400	Active TSS	Primary B cells from cord blood	blood
46	chr7:39605200-39605400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
47	chr7:39605200-39605400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr7:39605200-39605400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr7:39605200-39605400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr7:39605200-39605400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

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