Variant report

Variant	rs16862610
Chromosome Location	chr3:150052807-150052808
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:150049487..150053586-chr3:150054958..150059375,5	MCF-7	breast:
2	chr3:150048454..150052986-chr3:150087441..150091214,5	MCF-7	breast:
3	chr3:150046882..150048829-chr3:150050271..150053000,2	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1562788	1.00[CHB][hapmap]
rs1597466	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1597467	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16862607	1.00[CEU][hapmap];1.00[CHB][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]
rs2060662	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28454055	1.00[ASN][1000 genomes]
rs4301033	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59195912	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61217677	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62269236	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62271363	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62271364	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62271368	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62271395	1.00[ASN][1000 genomes]
rs6767155	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7614962	1.00[ASN][1000 genomes]
rs7616723	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7617025	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7617699	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7636643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9810244	1.00[ASN][1000 genomes]
rs9836480	1.00[CHB][hapmap]
rs9862778	1.00[CHB][hapmap];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829755	chr3:149992023-150156001	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16862610	ARHGEF26	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150033800-150053000	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr3:150043400-150059600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:150046600-150053200	Weak transcription	HSMMtube	muscle
4	chr3:150049600-150053200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:150049800-150053800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:150050800-150053800	Enhancers	NHEK	skin
7	chr3:150050800-150055200	Enhancers	HMEC	breast
8	chr3:150051400-150054000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr3:150052200-150053400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:150052400-150053200	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr3:150052400-150053400	Enhancers	Placenta Amnion	Placenta Amnion
12	chr3:150052400-150054000	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr3:150052400-150054000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:150052400-150054600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:150052600-150053000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:150052600-150053000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:150052600-150053600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr3:150052600-150054200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:150052600-150054800	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr3:150052800-150053000	Enhancers	Fetal Intestine Small	intestine
21	chr3:150052800-150053200	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr3:150052800-150054000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:150052800-150054000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:150052800-150054800	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr3:150052800-150055000	Enhancers	HUES64 Cell Line	embryonic stem cell

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