Variant report

Variant	rs6438003
Chromosome Location	chr3:111453889-111453890
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:111452077..111454237-chr3:111460686..111462940,2	K562	blood:
2	chr3:111453729..111455773-chr3:111578184..111580273,2	MCF-7	breast:
3	chr3:111448052..111452466-chr3:111452775..111456031,4	MCF-7	breast:
4	chr3:111452923..111457246-chr3:111577346..111581538,6	MCF-7	breast:
5	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: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10212300	0.85[EUR][1000 genomes]
rs10804492	0.81[CHD][hapmap]
rs10934106	0.82[CEU][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10934107	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs11711533	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11711582	0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12330761	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12490166	0.89[GIH][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs12490595	0.87[EUR][1000 genomes]
rs12496925	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12496971	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12632310	0.82[JPT][hapmap]
rs13069980	0.88[EUR][1000 genomes]
rs13074817	0.82[CEU][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13079085	0.82[CEU][hapmap];0.89[GIH][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4284954	0.82[CEU][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4431081	0.89[GIH][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4557129	0.81[CHD][hapmap]
rs4682299	0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4682303	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs56028731	0.99[ASN][1000 genomes]
rs62275532	0.99[ASN][1000 genomes]
rs6438008	0.83[EUR][1000 genomes]
rs6438009	0.84[EUR][1000 genomes]
rs6764720	0.82[EUR][1000 genomes]
rs6768713	0.82[CEU][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs6777540	0.86[EUR][1000 genomes]
rs6784753	0.87[GIH][hapmap]
rs6786386	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6788543	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6790072	0.84[EUR][1000 genomes]
rs6790079	0.86[EUR][1000 genomes]
rs6792493	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6796087	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6802995	0.88[EUR][1000 genomes]
rs7427201	0.87[EUR][1000 genomes]
rs7614443	0.87[EUR][1000 genomes]
rs7629156	0.81[CHD][hapmap]
rs955381	0.99[ASN][1000 genomes]
rs959540	0.99[ASN][1000 genomes]
rs9825915	0.86[EUR][1000 genomes]
rs9834030	0.82[CEU][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9838371	0.87[EUR][1000 genomes]
rs9863403	0.84[EUR][1000 genomes]
rs9868909	1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9870823	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]

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:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111415200-111454200	Weak transcription	Small Intestine	intestine
2	chr3:111427600-111456000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:111442000-111454200	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr3:111442400-111456000	Weak transcription	Lung	lung
5	chr3:111442800-111455800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr3:111443200-111454800	Weak transcription	Primary T cells from cord blood	blood
7	chr3:111444200-111456000	Weak transcription	Aorta	Aorta
8	chr3:111445200-111456800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:111448800-111454200	Weak transcription	Adipose Nuclei	Adipose
10	chr3:111449000-111454200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr3:111449000-111455800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr3:111449400-111456000	Weak transcription	Colon Smooth Muscle	Colon
13	chr3:111449600-111456000	Weak transcription	Esophagus	oesophagus
14	chr3:111451200-111454400	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr3:111451600-111460400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:111452200-111454200	Flanking Active TSS	A549	lung
17	chr3:111452200-111458200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:111452400-111454000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr3:111452400-111454800	Enhancers	Fetal Intestine Large	intestine
20	chr3:111452400-111455000	Enhancers	Stomach Mucosa	stomach
21	chr3:111452400-111456000	Weak transcription	Gastric	stomach
22	chr3:111452400-111458800	Enhancers	HMEC	breast
23	chr3:111452600-111454600	Flanking Active TSS	HepG2	liver
24	chr3:111452600-111455800	Weak transcription	Fetal Stomach	stomach
25	chr3:111452600-111457200	Enhancers	HSMM	muscle
26	chr3:111452800-111454000	Enhancers	Muscle Satellite Cultured Cells	--
27	chr3:111452800-111454800	Enhancers	Placenta	Placenta
28	chr3:111452800-111459200	Enhancers	Osteobl	bone
29	chr3:111452800-111460400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:111453000-111454200	Enhancers	Pancreas	Pancrea
31	chr3:111453000-111459400	Enhancers	Placenta Amnion	Placenta Amnion
32	chr3:111453200-111456200	Weak transcription	Fetal Kidney	kidney
33	chr3:111453400-111454000	Enhancers	Fetal Heart	heart
34	chr3:111453400-111454200	Enhancers	Fetal Intestine Small	intestine
35	chr3:111453400-111455800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:111453400-111458600	Enhancers	HSMMtube	muscle
37	chr3:111453600-111454200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr3:111453600-111454400	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr3:111453600-111454400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:111453600-111454800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:111453600-111454800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr3:111453600-111454800	Enhancers	Right Atrium	heart
43	chr3:111453600-111455000	Enhancers	HUVEC	blood vessel
44	chr3:111453600-111456800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:111453600-111456800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr3:111453600-111458800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:111453600-111458800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr3:111453600-111459000	Enhancers	NHDF-Ad	bronchial
49	chr3:111453800-111454000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr3:111453800-111454000	Enhancers	Hela-S3	cervix

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