Variant report

Variant	rs9503173
Chromosome Location	chr6:2399463-2399464
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10155673	1.00[AMR][1000 genomes]
rs10155682	0.95[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10155748	1.00[AMR][1000 genomes]
rs11964241	0.89[AMR][1000 genomes]
rs11964259	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11964680	0.95[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28633763	0.89[AMR][1000 genomes]
rs34500504	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56714114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57504362	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59455919	0.89[AMR][1000 genomes]
rs6925879	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73344778	0.89[AMR][1000 genomes]
rs73344794	0.89[AMR][1000 genomes]
rs73344796	0.89[AMR][1000 genomes]
rs73344799	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73346609	0.89[AMR][1000 genomes]
rs73346610	0.89[AMR][1000 genomes]
rs73346620	0.89[AMR][1000 genomes]
rs7739140	0.89[AMR][1000 genomes]
rs7744661	0.89[AMR][1000 genomes]
rs9501832	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9501833	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9501834	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9501835	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9503170	1.00[AMR][1000 genomes]
rs9503171	0.94[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9503172	1.00[AMR][1000 genomes]
rs9503174	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9503177	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9503178	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9503179	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9503181	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
2	nsv883388	chr6:2093432-2514911	Strong transcription Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
3	nsv883389	chr6:2093432-2776303	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
4	nsv1021573	chr6:2246721-2832408	Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
5	nsv538102	chr6:2246721-2832408	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
6	nsv883390	chr6:2265344-2584919	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv883391	chr6:2282747-2507448	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv1016878	chr6:2375784-2680476	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv498004	chr6:2380300-3313587	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	163 gene(s)	inside rSNPs	diseases
10	esv2763527	chr6:2390712-2400244	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2392400-2400600	Weak transcription	Aorta	Aorta
2	chr6:2392400-2414400	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr6:2395400-2403800	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr6:2396800-2400800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr6:2396800-2415400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr6:2397000-2399600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr6:2397000-2402800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr6:2397000-2409400	Weak transcription	HepG2	liver
9	chr6:2397200-2410200	Weak transcription	Colon Smooth Muscle	Colon
10	chr6:2397400-2402400	Weak transcription	Psoas Muscle	Psoas
11	chr6:2397400-2403000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr6:2397400-2404200	Weak transcription	Fetal Kidney	kidney
13	chr6:2397600-2399600	Strong transcription	Fetal Intestine Small	intestine
14	chr6:2397600-2399800	Strong transcription	Pancreas	Pancrea
15	chr6:2397800-2400000	Weak transcription	Brain Hippocampus Middle	brain
16	chr6:2397800-2400400	Weak transcription	Fetal Brain Female	brain
17	chr6:2397800-2406800	Weak transcription	Fetal Heart	heart
18	chr6:2398000-2399600	Weak transcription	Fetal Muscle Trunk	muscle
19	chr6:2398000-2399800	Strong transcription	Fetal Stomach	stomach
20	chr6:2398000-2400400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr6:2398000-2400800	Weak transcription	Adipose Nuclei	Adipose
22	chr6:2398000-2401000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr6:2398000-2401200	Weak transcription	Colonic Mucosa	Colon
24	chr6:2398000-2403200	Weak transcription	Brain Substantia Nigra	brain
25	chr6:2398000-2412600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:2398200-2399600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr6:2398200-2399600	Weak transcription	Fetal Muscle Leg	muscle
28	chr6:2398200-2400600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:2398200-2400800	Strong transcription	Liver	Liver
30	chr6:2398200-2401000	Strong transcription	Ovary	ovary
31	chr6:2398200-2405400	Weak transcription	Right Ventricle	heart
32	chr6:2398400-2401800	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr6:2398600-2403800	Weak transcription	Gastric	stomach
34	chr6:2398600-2405400	Weak transcription	Spleen	Spleen
35	chr6:2398800-2399800	Strong transcription	Stomach Smooth Muscle	stomach
36	chr6:2398800-2402200	Strong transcription	Left Ventricle	heart
37	chr6:2399000-2399800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:2399000-2400600	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr6:2399000-2401200	Strong transcription	Fetal Intestine Large	intestine
40	chr6:2399400-2399800	Strong transcription	Primary T cells from cord blood	blood
41	chr6:2399400-2399800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
42	chr6:2399400-2399800	ZNF genes & repeats	Fetal Lung	lung
43	chr6:2399400-2402400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links