Variant report

Variant	rs2276820
Chromosome Location	chr3:52867718-52867719
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10049313	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12637566	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13066997	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1986738	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1986739	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2001733	1.00[ASN][1000 genomes]
rs2001734	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs2245536	1.00[ASN][1000 genomes]
rs2246888	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2246889	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2256728	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2256734	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs2276811	1.00[CHD][hapmap]
rs2276814	1.00[ASN][1000 genomes]
rs2276816	1.00[LWK][hapmap]
rs2276819	1.00[ASN][1000 genomes]
rs2276821	1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs2276822	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs2336155	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs2336158	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2336159	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2336556	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2336557	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2336559	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs2535615	1.00[ASN][1000 genomes]
rs2535616	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2535617	1.00[ASN][1000 genomes]
rs2535618	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2535619	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs2535620	1.00[ASN][1000 genomes]
rs2535622	1.00[ASN][1000 genomes]
rs2535623	1.00[ASN][1000 genomes]
rs2535626	1.00[ASN][1000 genomes]
rs2535628	1.00[ASN][1000 genomes]
rs2535631	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2535632	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs2535636	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2535637	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs2535639	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2535641	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2535642	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2535643	1.00[ASN][1000 genomes]
rs2535644	0.82[ASN][1000 genomes]
rs2535645	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2535646	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2710318	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2710319	1.00[ASN][1000 genomes]
rs2710320	1.00[ASN][1000 genomes]
rs2710321	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2710324	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs2710325	0.90[ASN][1000 genomes]
rs2710328	0.89[ASN][1000 genomes]
rs2710333	1.00[CHD][hapmap]
rs2710341	1.00[ASN][1000 genomes]
rs2710344	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2878633	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs2878634	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2878636	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs34352685	0.89[ASN][1000 genomes]
rs3774361	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4234637	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4687555	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4687659	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4687661	1.00[ASN][1000 genomes]
rs4687665	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs4687666	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4687667	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4687670	1.00[ASN][1000 genomes]
rs4687671	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4687674	1.00[ASN][1000 genomes]
rs4687675	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6774869	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs6776990	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7623667	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7637212	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7647534	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7652476	1.00[ASN][1000 genomes]
rs9311482	1.00[CHD][hapmap]
rs9681089	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs9682819	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9819608	1.00[CHB][hapmap]
rs9822686	1.00[CHB][hapmap]
rs9842048	1.00[CHD][hapmap]
rs9861870	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
2	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv1810629	chr3:52817031-52869635	Weak transcription Active TSS Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv876797	chr3:52817675-52873984	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	esv3435205	chr3:52867536-52867892	Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Enhancers Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52850200-52868400	Weak transcription	Colonic Mucosa	Colon
2	chr3:52852200-52869200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr3:52852800-52869200	Weak transcription	Primary B cells from cord blood	blood
4	chr3:52853000-52868000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:52854200-52874200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:52854800-52869200	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr3:52854800-52888400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:52856000-52875000	Weak transcription	Fetal Intestine Large	intestine
9	chr3:52856400-52868200	Weak transcription	Fetal Lung	lung
10	chr3:52857000-52868600	Weak transcription	Primary B cells from peripheral blood	blood
11	chr3:52858000-52867800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:52858000-52868400	Weak transcription	Brain Germinal Matrix	brain
13	chr3:52858800-52868800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr3:52858800-52868800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:52858800-52869200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:52859400-52869000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr3:52860200-52869000	Weak transcription	Fetal Intestine Small	intestine
18	chr3:52861200-52868800	Weak transcription	Lung	lung
19	chr3:52862000-52869200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:52862000-52882600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr3:52863200-52872600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr3:52864400-52875800	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr3:52865000-52867800	Enhancers	Psoas Muscle	Psoas
24	chr3:52865000-52869400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr3:52865200-52869000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:52865600-52874200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr3:52865600-52875200	Weak transcription	Dnd41	blood
28	chr3:52865800-52869000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:52865800-52878600	Weak transcription	Small Intestine	intestine
30	chr3:52866000-52868200	Weak transcription	Brain Angular Gyrus	brain
31	chr3:52866000-52868400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr3:52866000-52869800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr3:52866000-52884800	Weak transcription	HMEC	breast
34	chr3:52866200-52867800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:52866200-52868200	Weak transcription	Ovary	ovary
36	chr3:52866200-52868400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr3:52866200-52868600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
38	chr3:52866200-52869000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:52866200-52869200	Weak transcription	Placenta	Placenta
40	chr3:52866200-52869600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:52866200-52870200	Weak transcription	Gastric	stomach
42	chr3:52866200-52872600	Weak transcription	Duodenum Mucosa	Duodenum
43	chr3:52866200-52872600	Weak transcription	Esophagus	oesophagus
44	chr3:52866200-52885200	Weak transcription	NHEK	skin
45	chr3:52866400-52867800	Weak transcription	Left Ventricle	heart
46	chr3:52866400-52867800	Weak transcription	Right Ventricle	heart
47	chr3:52866400-52868000	Strong transcription	Fetal Stomach	stomach
48	chr3:52866400-52868400	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr3:52866400-52868400	Weak transcription	Rectal Smooth Muscle	rectum
50	chr3:52866400-52868600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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