Variant report

Variant	rs11242716
Chromosome Location	chr6:1699662-1699663
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:1686716..1688297-chr6:1699129..1701507,3	MCF-7	breast:
2	chr6:1692499..1695604-chr6:1698340..1700844,3	K562	blood:
3	chr6:1687898..1689601-chr6:1699469..1701760,2	K562	blood:

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

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

rs_ID	r²[population]
rs12525841	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12526653	0.84[AFR][1000 genomes]
rs6596840	0.98[ASN][1000 genomes]
rs9328066	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9328067	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9378305	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9378306	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9378650	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9405505	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9503004	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9503006	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9503007	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9503008	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9503009	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9503010	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9503011	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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:32 , 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	chr6:1686600-1700000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:1686600-1700800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:1686800-1701600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:1688600-1706400	Weak transcription	Gastric	stomach
6	chr6:1690000-1701200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:1690000-1715000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr6:1690400-1703200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:1693400-1701600	Strong transcription	HepG2	liver
10	chr6:1693600-1718200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr6:1693800-1708400	Weak transcription	Fetal Intestine Small	intestine
12	chr6:1694000-1709400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr6:1694200-1724400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr6:1695400-1729400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr6:1695800-1731400	Weak transcription	Fetal Intestine Large	intestine
16	chr6:1696200-1705600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr6:1696400-1700000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:1696600-1699800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr6:1696600-1702400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:1697000-1700200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:1697000-1700200	Weak transcription	Osteobl	bone
22	chr6:1697000-1701200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr6:1697000-1702400	Weak transcription	Aorta	Aorta
24	chr6:1697200-1700000	Weak transcription	Fetal Muscle Leg	muscle
25	chr6:1699000-1700800	Weak transcription	Placenta	Placenta
26	chr6:1699200-1699800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
27	chr6:1699200-1699800	Enhancers	Primary T cells from cord blood	blood
28	chr6:1699400-1700600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr6:1699400-1701600	Weak transcription	Adipose Nuclei	Adipose
30	chr6:1699400-1703200	Weak transcription	Lung	lung
31	chr6:1699600-1699800	Enhancers	Spleen	Spleen
32	chr6:1699600-1700800	Enhancers	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links