Variant report

Variant	rs6715159
Chromosome Location	chr2:20784683-20784684
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20783319..20786192-chr2:20833674..20835720,2	MCF-7	breast:
2	chr2:20777247..20781087-chr2:20782458..20786081,5	K562	blood:
3	chr2:20769124..20771781-chr2:20783924..20785551,2	MCF-7	breast:
4	chr2:20645526..20651779-chr2:20782666..20787622,12	MCF-7	breast:
5	chr2:20783982..20787771-chr2:20790367..20794656,9	K562	blood:
6	chr2:20646487..20649741-chr2:20783299..20785992,4	MCF-7	breast:
7	chr2:20778242..20781356-chr2:20782083..20785108,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231948	Chromatin interaction
ENSG00000228950	Chromatin interaction
ENSG00000143878	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10153843	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10166792	0.82[JPT][hapmap]
rs10177787	0.80[JPT][hapmap]
rs10177834	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10195324	0.82[JPT][hapmap]
rs10195722	0.86[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs11096676	0.84[AFR][1000 genomes]
rs11096679	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11885969	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11897611	0.85[AFR][1000 genomes]
rs12472478	0.86[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs12621527	0.86[CHB][hapmap]
rs13013281	0.94[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13031724	0.94[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13032956	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1466200	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16987857	0.82[JPT][hapmap]
rs2882035	0.81[JPT][hapmap]
rs4666426	0.86[AFR][1000 genomes]
rs4666429	0.82[JPT][hapmap]
rs4666430	0.86[CHB][hapmap];0.82[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes]
rs4666431	0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs4666436	0.94[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57734601	0.87[ASN][1000 genomes]
rs6712435	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6722960	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs921599	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[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	nsv833537	chr2:20630092-20826816	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv833548	chr2:20682073-20864078	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1012037	chr2:20770850-20824893	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535598	chr2:20770850-20824893	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6715159		cis	Lymphoblastoid	GTEx
rs6715159	hmm27769	cis	multi-tissue	Pritchard

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20765800-20786200	Enhancers	HUVEC	blood vessel
2	chr2:20772600-20785800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:20778800-20784800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr2:20780000-20786000	Weak transcription	Small Intestine	intestine
5	chr2:20781600-20785400	Enhancers	Placenta Amnion	Placenta Amnion
6	chr2:20781600-20786000	Enhancers	Brain Hippocampus Middle	brain
7	chr2:20781800-20786000	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr2:20781800-20786000	Enhancers	Brain Anterior Caudate	brain
9	chr2:20781800-20786000	Enhancers	Brain Substantia Nigra	brain
10	chr2:20781800-20786200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:20781800-20786800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:20782000-20785400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr2:20782000-20785800	Enhancers	Brain Angular Gyrus	brain
14	chr2:20782000-20785800	Enhancers	K562	blood
15	chr2:20782000-20786000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:20782000-20786200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:20782000-20786200	Enhancers	Fetal Intestine Small	intestine
18	chr2:20782000-20787400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr2:20782200-20786200	Enhancers	Placenta	Placenta
20	chr2:20782200-20786400	Enhancers	Fetal Stomach	stomach
21	chr2:20782400-20785600	Enhancers	Fetal Intestine Large	intestine
22	chr2:20782400-20785800	Enhancers	Brain Cingulate Gyrus	brain
23	chr2:20782400-20786000	Enhancers	Left Ventricle	heart
24	chr2:20782400-20786000	Enhancers	Pancreas	Pancrea
25	chr2:20782400-20786000	Enhancers	Right Ventricle	heart
26	chr2:20782400-20786400	Enhancers	Right Atrium	heart
27	chr2:20782400-20786400	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr2:20782600-20785000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr2:20782600-20785000	Enhancers	Stomach Mucosa	stomach
30	chr2:20782600-20786000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:20782600-20786000	Enhancers	Spleen	Spleen
32	chr2:20782600-20787800	Enhancers	Adipose Nuclei	Adipose
33	chr2:20782800-20785200	Enhancers	Gastric	stomach
34	chr2:20782800-20785400	Enhancers	HMEC	breast
35	chr2:20782800-20785600	Enhancers	NH-A	brain
36	chr2:20782800-20786000	Enhancers	Lung	lung
37	chr2:20782800-20786200	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr2:20782800-20787400	Enhancers	Fetal Muscle Leg	muscle
39	chr2:20783000-20785800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:20783400-20785000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr2:20783400-20785400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr2:20783400-20785400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr2:20783400-20786800	Enhancers	NHDF-Ad	bronchial
44	chr2:20783600-20785000	Enhancers	H9 Cell Line	embryonic stem cell
45	chr2:20783600-20785200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:20783600-20785400	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr2:20783600-20785400	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr2:20783600-20785600	Enhancers	Fetal Kidney	kidney
49	chr2:20783600-20785800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr2:20783600-20786000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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