Variant report

Variant	rs16862607
Chromosome Location	chr3:150051298-150051299
allele	A/G
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	chr3:150049870..150052428-chr3:150123963..150126611,2	MCF-7	breast:
3	chr3:150049522..150052674-chr3:150126551..150129363,3	K562	blood:
4	chr3:150048454..150052986-chr3:150087441..150091214,5	MCF-7	breast:
5	chr3:150046882..150048829-chr3:150050271..150053000,2	K562	blood:

Variant related genes	Relation type
ENSG00000196428	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

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]
rs16862610	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];0.93[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];0.96[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

No data

Chromatin state (count:20 , 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	chr3:150042600-150051400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr3:150043400-150059600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:150043800-150052600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:150046600-150052400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr3:150046600-150053200	Weak transcription	HSMMtube	muscle
7	chr3:150046800-150052400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:150048000-150052400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:150048000-150052800	Weak transcription	Fetal Intestine Small	intestine
10	chr3:150049600-150053200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:150049800-150053800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:150050800-150051600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr3:150050800-150051800	Enhancers	A549	lung
14	chr3:150050800-150053800	Enhancers	NHEK	skin
15	chr3:150050800-150055200	Enhancers	HMEC	breast
16	chr3:150051000-150051800	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr3:150051000-150051800	Enhancers	Hela-S3	cervix
18	chr3:150051000-150052000	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr3:150051200-150051600	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr3:150051200-150051600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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