Variant report

Variant	rs9838166
Chromosome Location	chr3:98641443-98641444
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:98619561..98621947-chr3:98640525..98642623,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000057019	Chromatin interaction
ENSG00000239462	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10084679	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs12330381	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13317610	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13318960	0.85[AMR][1000 genomes]
rs13320266	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13320890	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs13322253	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13327449	0.88[EUR][1000 genomes]
rs13327485	0.88[EUR][1000 genomes]
rs28417568	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs28429424	0.82[ASN][1000 genomes]
rs28489284	0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs28528154	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28650813	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28821579	0.94[EUR][1000 genomes]
rs28883308	0.88[EUR][1000 genomes]
rs3796133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs56172805	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56857413	0.94[ASN][1000 genomes]
rs57962467	0.94[ASN][1000 genomes]
rs59906228	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72932691	0.82[ASN][1000 genomes]
rs72932700	0.83[ASN][1000 genomes]
rs72934623	0.88[ASN][1000 genomes]
rs72934641	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs72938540	0.86[EUR][1000 genomes]
rs72938577	0.94[ASN][1000 genomes]
rs9289696	0.86[EUR][1000 genomes]
rs9289699	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9289700	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9810407	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812438	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9818215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9819279	0.86[EUR][1000 genomes]
rs9819309	0.94[EUR][1000 genomes]
rs9828045	0.94[EUR][1000 genomes]
rs9833945	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836437	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838238	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838706	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9839559	1.00[CEU][hapmap]
rs9842226	0.86[EUR][1000 genomes]
rs9848335	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9848583	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850469	0.86[EUR][1000 genomes]
rs9852889	0.86[EUR][1000 genomes]
rs9859042	0.86[EUR][1000 genomes]
rs9862660	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9864010	0.86[EUR][1000 genomes]
rs9870500	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs9870940	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9872073	0.85[EUR][1000 genomes]
rs9872301	0.88[EUR][1000 genomes]
rs9879302	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9883751	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:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98626600-98641600	Weak transcription	NHLF	lung
2	chr3:98635600-98641600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr3:98636400-98643600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:98639200-98642200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:98640000-98642800	Enhancers	NHEK	skin
6	chr3:98640000-98643000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:98640200-98643000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:98640400-98643200	Enhancers	Hela-S3	cervix
9	chr3:98640400-98643600	Enhancers	HMEC	breast
10	chr3:98640600-98641600	Enhancers	Muscle Satellite Cultured Cells	--
11	chr3:98640600-98642400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:98640600-98642400	Enhancers	NHDF-Ad	bronchial
13	chr3:98640600-98642600	Enhancers	Osteobl	bone
14	chr3:98640600-98642800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:98640600-98643200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:98640800-98642000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:98640800-98642400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:98640800-98642600	Enhancers	HUVEC	blood vessel
19	chr3:98640800-98642600	Enhancers	NH-A	brain
20	chr3:98640800-98642800	Enhancers	HSMM	muscle
21	chr3:98640800-98643200	Flanking Active TSS	A549	lung
22	chr3:98641000-98641800	Flanking Active TSS	Fetal Heart	heart
23	chr3:98641000-98642400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:98641400-98641800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr3:98641400-98642200	Enhancers	HSMMtube	muscle

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