Variant report

Variant	rs9868909
Chromosome Location	chr3:111454845-111454846
allele	G/T
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]
rs10470303	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11710738	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11711533	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11711582	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12330761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12490166	0.98[GIH][hapmap]
rs12632310	0.82[JPT][hapmap]
rs13074817	0.98[GIH][hapmap]
rs13079085	0.98[GIH][hapmap]
rs2137595	0.96[CEU][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs4284954	0.98[GIH][hapmap]
rs4401340	0.93[TSI][hapmap]
rs4413291	0.96[CEU][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs4431081	0.98[GIH][hapmap]
rs4682057	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4682298	0.82[CEU][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs4682299	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4682303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4682305	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4682312	0.88[CEU][hapmap]
rs4682314	0.88[CEU][hapmap]
rs56028731	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62273780	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62275532	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438003	1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6768713	0.98[GIH][hapmap]
rs6784753	1.00[CEU][hapmap];0.95[GIH][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6786612	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6788543	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6796087	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7609653	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs955381	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs959540	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818574	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9823974	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9834030	0.98[GIH][hapmap]
rs9868171	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9870656	0.87[CEU][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:54 , 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	chr3:111444200-111456000	Weak transcription	Aorta	Aorta
5	chr3:111445200-111456800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:111449000-111455800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr3:111449400-111456000	Weak transcription	Colon Smooth Muscle	Colon
8	chr3:111449600-111456000	Weak transcription	Esophagus	oesophagus
9	chr3:111451600-111460400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:111452200-111458200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:111452400-111455000	Enhancers	Stomach Mucosa	stomach
12	chr3:111452400-111456000	Weak transcription	Gastric	stomach
13	chr3:111452400-111458800	Enhancers	HMEC	breast
14	chr3:111452600-111455800	Weak transcription	Fetal Stomach	stomach
15	chr3:111452600-111457200	Enhancers	HSMM	muscle
16	chr3:111452800-111459200	Enhancers	Osteobl	bone
17	chr3:111452800-111460400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:111453000-111459400	Enhancers	Placenta Amnion	Placenta Amnion
19	chr3:111453200-111456200	Weak transcription	Fetal Kidney	kidney
20	chr3:111453400-111455800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:111453400-111458600	Enhancers	HSMMtube	muscle
22	chr3:111453600-111455000	Enhancers	HUVEC	blood vessel
23	chr3:111453600-111456800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:111453600-111456800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:111453600-111458800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:111453600-111458800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:111453600-111459000	Enhancers	NHDF-Ad	bronchial
28	chr3:111453800-111456600	Enhancers	NHLF	lung
29	chr3:111453800-111457600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr3:111453800-111457600	Enhancers	NHEK	skin
31	chr3:111454000-111455000	Enhancers	Duodenum Mucosa	Duodenum
32	chr3:111454200-111455600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:111454200-111455800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:111454200-111455800	Weak transcription	Pancreas	Pancrea
35	chr3:111454200-111456000	Weak transcription	Fetal Intestine Small	intestine
36	chr3:111454200-111456800	Enhancers	NH-A	brain
37	chr3:111454200-111458200	Enhancers	Hela-S3	cervix
38	chr3:111454400-111455000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr3:111454400-111455600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:111454600-111455600	Weak transcription	Adipose Nuclei	Adipose
41	chr3:111454600-111455800	Weak transcription	Small Intestine	intestine
42	chr3:111454600-111458000	Enhancers	Muscle Satellite Cultured Cells	--
43	chr3:111454600-111459400	Enhancers	HepG2	liver
44	chr3:111454600-111459600	Enhancers	Liver	Liver
45	chr3:111454800-111455000	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr3:111454800-111455000	Enhancers	Primary T cells from cord blood	blood
47	chr3:111454800-111455200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:111454800-111455600	Weak transcription	Right Atrium	heart
49	chr3:111454800-111455800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:111454800-111455800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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