Variant report

Variant	rs2697662
Chromosome Location	chr5:50024899-50024900
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 148 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs10038842	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10039639	0.91[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10041633	1.00[ASN][1000 genomes]
rs10043477	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10045122	1.00[ASN][1000 genomes]
rs10052001	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10065069	0.97[AMR][1000 genomes]
rs10070517	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10071272	1.00[ASN][1000 genomes]
rs10434558	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs10471888	1.00[ASN][1000 genomes]
rs10471893	1.00[ASN][1000 genomes]
rs10471940	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10471956	1.00[CEU][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10755235	0.90[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10940472	0.92[EUR][1000 genomes]
rs10940497	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs11739828	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11741205	1.00[ASN][1000 genomes]
rs11750241	0.92[EUR][1000 genomes]
rs11750771	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12188262	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12188654	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12518710	1.00[ASN][1000 genomes]
rs12519006	0.86[EUR][1000 genomes]
rs12521579	0.86[EUR][1000 genomes]
rs13153982	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13162921	1.00[ASN][1000 genomes]
rs13164951	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13173734	0.92[EUR][1000 genomes]
rs13355372	1.00[ASN][1000 genomes]
rs13355434	1.00[ASN][1000 genomes]
rs13359044	0.86[EUR][1000 genomes]
rs1375127	1.00[CEU][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs152102	0.86[EUR][1000 genomes]
rs154133	0.86[EUR][1000 genomes]
rs154135	0.85[EUR][1000 genomes]
rs154137	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs154138	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs154141	0.86[EUR][1000 genomes]
rs157970	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs16884018	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs169497	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs171555	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs17195388	0.86[EUR][1000 genomes]
rs182230	1.00[CEU][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1839128	0.91[CEU][hapmap]
rs1988613	1.00[CEU][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2034392	1.00[ASN][1000 genomes]
rs2034394	1.00[ASN][1000 genomes]
rs2354526	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2548581	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2548582	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs2548583	0.85[EUR][1000 genomes]
rs256340	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs256341	1.00[CEU][hapmap];0.82[YRI][hapmap];0.86[EUR][1000 genomes]
rs26062	0.92[CEU][hapmap]
rs26065	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs26066	0.95[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26068	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26069	1.00[CEU][hapmap];0.82[YRI][hapmap];0.84[EUR][1000 genomes]
rs26071	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs27156	0.82[EUR][1000 genomes]
rs27244	0.84[EUR][1000 genomes]
rs27245	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs27251	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs27254	0.84[EUR][1000 genomes]
rs27357	0.83[EUR][1000 genomes]
rs27465	0.85[EUR][1000 genomes]
rs27467	1.00[CEU][hapmap]
rs27468	1.00[CEU][hapmap];0.89[YRI][hapmap];0.86[EUR][1000 genomes]
rs27469	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs27574	0.82[EUR][1000 genomes]
rs27627	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs27725	0.83[EUR][1000 genomes]
rs28085	0.83[EUR][1000 genomes]
rs282549	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs282550	1.00[CEU][hapmap];0.83[YRI][hapmap];0.86[EUR][1000 genomes]
rs282551	0.85[EUR][1000 genomes]
rs282552	1.00[CEU][hapmap];0.83[YRI][hapmap];0.86[EUR][1000 genomes]
rs282553	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs282557	0.92[EUR][1000 genomes]
rs282559	1.00[CEU][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs282561	1.00[CEU][hapmap];0.90[YRI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs32377	0.95[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32378	0.95[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs32404	0.86[CEU][hapmap]
rs32425	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs3763367	0.88[EUR][1000 genomes]
rs39613	1.00[CEU][hapmap];0.83[YRI][hapmap];0.84[EUR][1000 genomes]
rs4029420	1.00[CEU][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4101529	1.00[ASN][1000 genomes]
rs42284	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs4865628	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4865846	1.00[ASN][1000 genomes]
rs4866001	1.00[ASN][1000 genomes]
rs57079776	0.85[EUR][1000 genomes]
rs578198	0.92[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs62366937	0.90[EUR][1000 genomes]
rs6450301	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6450359	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6869356	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6872496	1.00[CEU][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6879306	1.00[ASN][1000 genomes]
rs6886872	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6888147	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6890519	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6890869	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs73093361	1.00[ASN][1000 genomes]
rs73112331	1.00[ASN][1000 genomes]
rs73112340	1.00[ASN][1000 genomes]
rs7449019	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7709831	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7710150	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7711839	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7723361	0.83[CEU][hapmap];1.00[YRI][hapmap]
rs7728222	1.00[ASN][1000 genomes]
rs7730847	1.00[ASN][1000 genomes]
rs7734389	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs895801	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs921210	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016583	chr5:49455624-50116720	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1023140	chr5:49455624-50121623	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv918220	chr5:49584188-50111282	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv931010	chr5:49584189-50118254	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv523212	chr5:49597497-50058043	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv2757995	chr5:49748352-50058182	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	esv2759342	chr5:49748352-50058182	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv462159	chr5:49960673-50229851	Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv598108	chr5:49960673-50229851	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv537759	chr5:49986171-50033616	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv1030068	chr5:49986171-50047352	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv537760	chr5:49986171-50047352	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv1016237	chr5:49986171-50118816	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
14	nsv537761	chr5:49986171-50118816	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
15	nsv1034445	chr5:49986171-50492609	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
16	nsv521214	chr5:49988020-50037381	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
17	nsv462160	chr5:49988020-50058043	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
18	nsv598109	chr5:49988020-50058043	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
19	nsv598110	chr5:49988020-50089919	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
20	nsv462162	chr5:49989701-50040778	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
21	nsv598111	chr5:49989701-50040778	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
22	nsv598112	chr5:49989701-50062611	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
23	nsv462163	chr5:49989701-50088317	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
24	nsv598113	chr5:49989701-50088317	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
25	nsv598114	chr5:49991561-50088317	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
26	nsv462164	chr5:50017724-50063035	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
27	nsv598115	chr5:50017724-50063035	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2697662	LOC647121	Cis_1M	lymphoblastoid	RTeQTL
rs2697662	PARP8	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:50007800-50031000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr5:50014400-50036000	Weak transcription	Primary B cells from cord blood	blood
3	chr5:50016800-50025400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:50016800-50025600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr5:50018800-50026600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:50019000-50025200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr5:50021200-50026000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr5:50021400-50027400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr5:50022600-50026200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr5:50022800-50025800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr5:50023200-50026800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr5:50023200-50036400	Weak transcription	Pancreas	Pancrea
13	chr5:50023200-50038400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr5:50023400-50025400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr5:50023400-50025800	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr5:50023400-50026600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr5:50023400-50026600	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr5:50023400-50038600	Weak transcription	Primary B cells from peripheral blood	blood
19	chr5:50023400-50040200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr5:50024000-50025000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr5:50024000-50025000	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr5:50024000-50025000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr5:50024000-50026600	Weak transcription	Stomach Mucosa	stomach
24	chr5:50024000-50028800	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr5:50024000-50034600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr5:50024000-50038200	Weak transcription	Primary T cells from cord blood	blood
27	chr5:50024000-50038600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr5:50024000-50040000	Weak transcription	Small Intestine	intestine
29	chr5:50024200-50025000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr5:50024200-50026200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr5:50024200-50032400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr5:50024800-50025800	Enhancers	Primary T helper naive cells from peripheral blood	blood

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