Variant report

Variant	rs7620801
Chromosome Location	chr3:111454533-111454534
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:111453729..111455773-chr3:111578184..111580273,2	MCF-7	breast:
2	chr3:111448052..111452466-chr3:111452775..111456031,4	MCF-7	breast:
3	chr3:111452923..111457246-chr3:111577346..111581538,6	MCF-7	breast:
4	chr3:111448469..111451104-chr3:111452736..111455582,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144824	Chromatin interaction
ENSG00000240891	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10934104	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11709591	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11917956	1.00[TSI][hapmap]
rs12638437	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1398749	1.00[ASN][1000 genomes]
rs1398752	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1398755	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1513332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1513333	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1513334	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17281318	1.00[MEX][hapmap]
rs2399395	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[LWK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs35840064	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35894167	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4234402	1.00[ASN][1000 genomes]
rs4450776	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs4682055	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682062	1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs4682297	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4682300	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682301	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57628489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60556634	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6438002	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6768082	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6791600	0.85[CEU][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6800228	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7427989	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7636559	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7640416	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7642808	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7643067	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7644696	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7648126	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7650348	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs7651391	0.82[CEU][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7653881	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs951338	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[LWK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv591290	chr3:111427455-111462570	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111427600-111456000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:111442400-111456000	Weak transcription	Lung	lung
3	chr3:111442800-111455800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr3:111443200-111454800	Weak transcription	Primary T cells from cord blood	blood
5	chr3:111444200-111456000	Weak transcription	Aorta	Aorta
6	chr3:111445200-111456800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:111449000-111455800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr3:111449400-111456000	Weak transcription	Colon Smooth Muscle	Colon
9	chr3:111449600-111456000	Weak transcription	Esophagus	oesophagus
10	chr3:111451600-111460400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:111452200-111458200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:111452400-111454800	Enhancers	Fetal Intestine Large	intestine
13	chr3:111452400-111455000	Enhancers	Stomach Mucosa	stomach
14	chr3:111452400-111456000	Weak transcription	Gastric	stomach
15	chr3:111452400-111458800	Enhancers	HMEC	breast
16	chr3:111452600-111454600	Flanking Active TSS	HepG2	liver
17	chr3:111452600-111455800	Weak transcription	Fetal Stomach	stomach
18	chr3:111452600-111457200	Enhancers	HSMM	muscle
19	chr3:111452800-111454800	Enhancers	Placenta	Placenta
20	chr3:111452800-111459200	Enhancers	Osteobl	bone
21	chr3:111452800-111460400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:111453000-111459400	Enhancers	Placenta Amnion	Placenta Amnion
23	chr3:111453200-111456200	Weak transcription	Fetal Kidney	kidney
24	chr3:111453400-111455800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:111453400-111458600	Enhancers	HSMMtube	muscle
26	chr3:111453600-111454800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:111453600-111454800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr3:111453600-111454800	Enhancers	Right Atrium	heart
29	chr3:111453600-111455000	Enhancers	HUVEC	blood vessel
30	chr3:111453600-111456800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:111453600-111456800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:111453600-111458800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:111453600-111458800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:111453600-111459000	Enhancers	NHDF-Ad	bronchial
35	chr3:111453800-111456600	Enhancers	NHLF	lung
36	chr3:111453800-111457600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr3:111453800-111457600	Enhancers	NHEK	skin
38	chr3:111454000-111454600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:111454000-111454800	Flanking Active TSS	Fetal Heart	heart
40	chr3:111454000-111455000	Enhancers	Duodenum Mucosa	Duodenum
41	chr3:111454200-111454600	Enhancers	Adipose Nuclei	Adipose
42	chr3:111454200-111454600	Flanking Active TSS	Liver	Liver
43	chr3:111454200-111454600	Enhancers	Small Intestine	intestine
44	chr3:111454200-111454600	Active TSS	A549	lung
45	chr3:111454200-111454800	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr3:111454200-111455600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr3:111454200-111455800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr3:111454200-111455800	Weak transcription	Pancreas	Pancrea
49	chr3:111454200-111456000	Weak transcription	Fetal Intestine Small	intestine
50	chr3:111454200-111456800	Enhancers	NH-A	brain

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