Variant report

Variant	rs11958752
Chromosome Location	chr5:37145808-37145809
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10037834	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10043395	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10052880	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10056009	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10057270	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10068328	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10068501	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10069109	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10072064	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10072288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10076911	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10473043	0.81[MEX][hapmap]
rs10805625	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10941320	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10941322	0.96[ASN][1000 genomes]
rs12108953	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12110010	1.00[CEU][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12110069	1.00[EUR][1000 genomes]
rs12186733	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12515518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12515522	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12515577	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12518867	0.82[CEU][hapmap];0.82[ASN][1000 genomes]
rs12520562	0.85[EUR][1000 genomes]
rs13356615	0.82[ASN][1000 genomes]
rs150594	0.81[MEX][hapmap]
rs16903477	0.85[EUR][1000 genomes]
rs16903526	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16903578	1.00[CEU][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[ASN][1000 genomes]
rs2055129	1.00[CEU][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2081109	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2272601	0.83[TSI][hapmap]
rs2365910	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2365912	0.82[ASN][1000 genomes]
rs2366275	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs301861	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs301862	1.00[CEU][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs301864	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs301866	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs301868	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs301870	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs301871	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs301876	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs301877	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs301890	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];0.84[YRI][hapmap];0.93[AFR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs301891	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs301892	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs301893	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs301894	0.89[EUR][1000 genomes]
rs301895	0.92[ASW][hapmap];1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs301902	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs301903	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs301904	0.92[ASW][hapmap];1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs301907	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs301910	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs301911	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs301914	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs301915	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs301916	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3822471	0.87[CEU][hapmap]
rs3849756	0.85[EUR][1000 genomes]
rs6859227	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6897283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73750950	0.97[EUR][1000 genomes]
rs7712984	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7724454	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9292649	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9687825	1.00[CEU][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525478	chr5:36804225-37349895	Strong transcription Transcr. at gene 5' and 3' Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	esv1793961	chr5:36866835-37361728	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv530225	chr5:36886635-37331912	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv1024051	chr5:36899712-37303001	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv537725	chr5:36899712-37303001	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv530226	chr5:36906377-37606367	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	esv1802391	chr5:36958598-37242600	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv597822	chr5:36997953-37147152	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
9	nsv534064	chr5:37054962-37586210	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
10	nsv881511	chr5:37088627-37552852	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
11	nsv597823	chr5:37111565-37430365	Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
12	nsv1026554	chr5:37112133-37734859	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
13	nsv537726	chr5:37112133-37734859	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
14	nsv1025988	chr5:37115142-37586211	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
15	nsv537727	chr5:37115142-37586211	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11958752	C6	cis	cerebellum	SCAN
rs11958752	C5orf42	cis	lymphoblastoid	seeQTL
rs11958752	C5orf42	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:37082800-37169200	Weak transcription	Spleen	Spleen
2	chr5:37105800-37156200	Weak transcription	NHLF	lung
3	chr5:37106200-37150200	Weak transcription	NHEK	skin
4	chr5:37112200-37198200	Weak transcription	Small Intestine	intestine
5	chr5:37113600-37222200	Weak transcription	Psoas Muscle	Psoas
6	chr5:37113800-37157000	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr5:37114600-37165400	Weak transcription	HMEC	breast
8	chr5:37118600-37153600	Weak transcription	Pancreas	Pancrea
9	chr5:37122000-37156000	Weak transcription	Brain Substantia Nigra	brain
10	chr5:37122800-37150800	Weak transcription	Fetal Heart	heart
11	chr5:37124200-37149400	Weak transcription	NH-A	brain
12	chr5:37133200-37169400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr5:37134200-37171200	Weak transcription	Colonic Mucosa	Colon
14	chr5:37135400-37146200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr5:37136200-37197200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr5:37136800-37170000	Weak transcription	Esophagus	oesophagus
17	chr5:37137400-37174000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr5:37137600-37169000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr5:37138000-37150200	Weak transcription	Primary T cells from cord blood	blood
20	chr5:37138000-37156000	Weak transcription	Aorta	Aorta
21	chr5:37138000-37157000	Weak transcription	Colon Smooth Muscle	Colon
22	chr5:37138400-37148400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr5:37138400-37155200	Weak transcription	Brain Angular Gyrus	brain
24	chr5:37138400-37156800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr5:37138400-37196800	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr5:37138600-37150400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr5:37138600-37150600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr5:37138600-37153400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr5:37138600-37179600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr5:37138800-37156800	Weak transcription	HUVEC	blood vessel
31	chr5:37139000-37150200	Weak transcription	Liver	Liver
32	chr5:37139000-37150200	Weak transcription	Brain Anterior Caudate	brain
33	chr5:37139000-37150600	Weak transcription	Primary B cells from cord blood	blood
34	chr5:37139000-37151800	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr5:37139000-37152200	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr5:37140000-37150200	Weak transcription	Right Ventricle	heart
37	chr5:37140000-37151800	Weak transcription	Thymus	Thymus
38	chr5:37141400-37147600	Weak transcription	Stomach Smooth Muscle	stomach
39	chr5:37141400-37150200	Weak transcription	Left Ventricle	heart
40	chr5:37141800-37147800	Weak transcription	Fetal Lung	lung
41	chr5:37142400-37151000	Weak transcription	NHDF-Ad	bronchial
42	chr5:37143000-37146200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr5:37143000-37153400	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr5:37143200-37149800	Weak transcription	Brain Hippocampus Middle	brain
45	chr5:37143200-37150200	Weak transcription	HSMMtube	muscle
46	chr5:37143400-37189600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr5:37143600-37156000	Weak transcription	Primary B cells from peripheral blood	blood
48	chr5:37143600-37157200	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr5:37143800-37150400	Weak transcription	Fetal Kidney	kidney
50	chr5:37143800-37150600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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