Variant report

Variant	rs10258946
Chromosome Location	chr7:39632682-39632683
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:39632294..39634662-chr7:39653376..39655988,2	K562	blood:
2	chr7:39630501..39633434-chr7:39759020..39762831,5	K562	blood:
3	chr10:3888800..3889300-chr7:39632378..39632982,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10236547	0.89[EUR][1000 genomes]
rs10245247	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10266149	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10486798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10486800	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs12111908	1.00[ASN][1000 genomes]
rs17171603	0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs17416652	1.00[CEU][hapmap]
rs17507685	1.00[CEU][hapmap]
rs17507748	1.00[CEU][hapmap]
rs17508696	1.00[CEU][hapmap]
rs17713754	0.84[ASN][1000 genomes]
rs17713951	0.88[ASN][1000 genomes]
rs17714049	1.00[ASN][1000 genomes]
rs17770594	0.84[ASN][1000 genomes]
rs17770612	0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs17770625	0.84[ASN][1000 genomes]
rs1989533	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2329455	0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs2329460	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2329461	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329463	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723881	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4723883	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4723884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4723885	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58299139	0.84[ASN][1000 genomes]
rs59071947	0.84[ASN][1000 genomes]
rs61493712	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6968742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73375695	0.84[ASN][1000 genomes]
rs7777173	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs7785964	0.84[ASN][1000 genomes]
rs7796063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7807233	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv966713	chr7:39629620-39638513	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39618400-39633000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:39626400-39635800	Enhancers	HUVEC	blood vessel
3	chr7:39627000-39633200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr7:39629400-39637000	Weak transcription	Stomach Mucosa	stomach
5	chr7:39629600-39640400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr7:39629600-39641800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr7:39629800-39634600	Weak transcription	Adipose Nuclei	Adipose
8	chr7:39630600-39633200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr7:39631400-39633800	Enhancers	Muscle Satellite Cultured Cells	--
10	chr7:39631400-39634000	Enhancers	HSMMtube	muscle
11	chr7:39631600-39633000	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr7:39631600-39633200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr7:39631800-39633200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr7:39632000-39632800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr7:39632000-39632800	Enhancers	NHEK	skin
16	chr7:39632000-39633000	Enhancers	NH-A	brain
17	chr7:39632000-39633200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr7:39632400-39632800	Weak transcription	HSMM	muscle
19	chr7:39632600-39632800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr7:39632600-39632800	Enhancers	NHDF-Ad	bronchial
21	chr7:39632600-39632800	Enhancers	Osteobl	bone
22	chr7:39632600-39633000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr7:39632600-39633200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr7:39632600-39633200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr7:39632600-39634000	Weak transcription	NHLF	lung
26	chr7:39632600-39634800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr7:39632600-39646000	Weak transcription	K562	blood

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