Variant report

Variant	rs9503009
Chromosome Location	chr6:1701839-1701840
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11242716	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12525841	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12526653	0.81[AFR][1000 genomes]
rs6596840	0.97[ASN][1000 genomes]
rs9328066	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9328067	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9378305	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9378306	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9378650	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9405505	0.84[ASW][hapmap];0.85[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9503004	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9503006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9503007	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9503008	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9503010	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9503011	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024111	chr6:1231850-1730146	Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1021924	chr6:1254891-1736995	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv538082	chr6:1254891-1736995	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
5	nsv491607	chr6:1580681-1951526	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1016594	chr6:1590030-1702529	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv530888	chr6:1605768-1739933	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv1015682	chr6:1661111-1717786	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv538092	chr6:1661111-1717786	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv462611	chr6:1688391-1702106	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv600808	chr6:1688391-1702106	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv432843	chr6:1694719-1725261	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv1020603	chr6:1697548-1921374	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv538093	chr6:1697548-1921374	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1679600-1715600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr6:1688600-1706400	Weak transcription	Gastric	stomach
3	chr6:1690000-1715000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr6:1690400-1703200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:1693600-1718200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr6:1693800-1708400	Weak transcription	Fetal Intestine Small	intestine
7	chr6:1694000-1709400	Weak transcription	Duodenum Mucosa	Duodenum
8	chr6:1694200-1724400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr6:1695400-1729400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr6:1695800-1731400	Weak transcription	Fetal Intestine Large	intestine
11	chr6:1696200-1705600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr6:1696600-1702400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr6:1697000-1702400	Weak transcription	Aorta	Aorta
14	chr6:1699400-1703200	Weak transcription	Lung	lung
15	chr6:1699800-1709200	Weak transcription	Spleen	Spleen
16	chr6:1699800-1716600	Weak transcription	Primary T cells from cord blood	blood
17	chr6:1700000-1702400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:1700000-1703400	Enhancers	Fetal Muscle Leg	muscle
19	chr6:1700200-1702400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:1700200-1702400	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr6:1700200-1702400	Enhancers	Osteobl	bone
22	chr6:1700400-1702800	Weak transcription	Right Atrium	heart
23	chr6:1700600-1702200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr6:1700600-1705800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr6:1700800-1702400	Enhancers	HSMM	muscle
26	chr6:1700800-1703400	Enhancers	NHLF	lung
27	chr6:1701000-1702200	Enhancers	Muscle Satellite Cultured Cells	--
28	chr6:1701000-1702200	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr6:1701000-1702200	Enhancers	NH-A	brain
30	chr6:1701200-1702000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr6:1701200-1702000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr6:1701200-1702000	Enhancers	HSMMtube	muscle
33	chr6:1701200-1702200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr6:1701200-1702200	Enhancers	HMEC	breast
35	chr6:1701200-1702400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:1701200-1749400	Weak transcription	Colonic Mucosa	Colon
37	chr6:1701400-1703200	Enhancers	NHDF-Ad	bronchial
38	chr6:1701600-1702000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr6:1701600-1702000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:1701600-1702000	Weak transcription	Fetal Muscle Trunk	muscle
41	chr6:1701600-1702000	Weak transcription	Placenta	Placenta
42	chr6:1701600-1702200	Enhancers	Colon Smooth Muscle	Colon
43	chr6:1701600-1702400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr6:1701600-1702600	Weak transcription	HepG2	liver
45	chr6:1701600-1703600	Enhancers	Adipose Nuclei	Adipose
46	chr6:1701600-1703600	Enhancers	Rectal Smooth Muscle	rectum
47	chr6:1701600-1703600	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr6:1701600-1703800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr6:1701600-1704800	Enhancers	Placenta Amnion	Placenta Amnion

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