Variant report

Variant	rs672460
Chromosome Location	chr11:77664156-77664157
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10751278	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10793265	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10899405	0.88[ASW][hapmap];0.85[CEU][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap]
rs10899406	0.88[ASW][hapmap];0.85[CEU][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap]
rs10899408	0.85[CEU][hapmap]
rs10899409	0.88[ASW][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap]
rs11237295	0.88[ASW][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap]
rs11237339	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11237340	0.95[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1783546	0.88[ASW][hapmap];0.85[CEU][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap]
rs1790246	0.88[ASW][hapmap];0.82[CHD][hapmap];0.88[GIH][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap]
rs1790250	1.00[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap];0.91[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1793343	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.82[EUR][1000 genomes]
rs1823508	0.81[JPT][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2034499	0.88[ASW][hapmap];0.90[CEU][hapmap];0.89[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2276441	0.95[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2510963	0.81[AMR][1000 genomes]
rs2510967	0.85[CEU][hapmap]
rs3018164	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3018412	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4245453	0.88[ASW][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap]
rs597346	0.90[CEU][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs628198	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs630274	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs630711	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6592747	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6592752	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6592753	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6592756	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs669869	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7110670	1.00[ASW][hapmap];0.95[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7127510	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7931272	0.88[CEU][hapmap]
rs7931392	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7938133	1.00[ASW][hapmap];0.95[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7938648	0.94[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7941732	0.94[CEU][hapmap];0.81[CHB][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9988883	0.88[ASW][hapmap];0.85[CEU][hapmap];0.80[CHD][hapmap];0.93[GIH][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050891	chr11:77416645-77788002	Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription 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 miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1037292	chr11:77431583-77745934	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription 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 miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv541092	chr11:77431583-77745934	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv949316	chr11:77454076-77769885	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv520740	chr11:77553638-77997936	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv1035753	chr11:77577384-77866386	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers 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	52 gene(s)	inside rSNPs	diseases
7	nsv541093	chr11:77577384-77866386	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv975205	chr11:77628075-77671380	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv8841	chr11:77641044-77692578	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs672460	INTS4	Cis_1M	lymphoblastoid	RTeQTL
rs672460	INTS4	cis	multi-tissue	Pritchard
rs672460	INTS4	cis	cerebellum	SCAN
rs672460	INTS4	cis	parietal	SCAN
rs672460	AQP11	cis	parietal	SCAN
rs672460	PAK1	cis	cerebellum	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77583400-77670600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr11:77583400-77690000	Weak transcription	Colonic Mucosa	Colon
3	chr11:77592800-77690000	Weak transcription	Small Intestine	intestine
4	chr11:77595800-77671000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr11:77597800-77669800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr11:77597800-77671000	Weak transcription	Fetal Brain Male	brain
7	chr11:77597800-77678200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr11:77597800-77690000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:77597800-77690000	Weak transcription	Esophagus	oesophagus
10	chr11:77597800-77690000	Weak transcription	Gastric	stomach
11	chr11:77602800-77690000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr11:77614800-77700200	Weak transcription	Psoas Muscle	Psoas
13	chr11:77618200-77668200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr11:77619000-77667000	Weak transcription	Fetal Kidney	kidney
15	chr11:77619000-77668000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr11:77625800-77665600	Weak transcription	HSMMtube	muscle
17	chr11:77625800-77697400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr11:77626000-77666200	Weak transcription	Brain Substantia Nigra	brain
19	chr11:77626000-77690000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr11:77626200-77665400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr11:77626200-77689400	Weak transcription	Colon Smooth Muscle	Colon
22	chr11:77626600-77665600	Weak transcription	Ovary	ovary
23	chr11:77626600-77689600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr11:77626600-77690000	Weak transcription	Pancreas	Pancrea
25	chr11:77627800-77684800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr11:77628000-77671000	Weak transcription	HSMM	muscle
27	chr11:77628400-77668000	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr11:77629400-77668000	Weak transcription	Aorta	Aorta
29	chr11:77630000-77665400	Weak transcription	Lung	lung
30	chr11:77630200-77669600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr11:77630600-77665400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr11:77638200-77665400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr11:77638200-77665600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr11:77638600-77665400	Weak transcription	Placenta	Placenta
35	chr11:77639400-77665400	Weak transcription	Stomach Smooth Muscle	stomach
36	chr11:77639400-77667000	Weak transcription	Fetal Lung	lung
37	chr11:77639400-77670200	Weak transcription	Brain Cingulate Gyrus	brain
38	chr11:77639800-77668000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr11:77640000-77667800	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr11:77641200-77669600	Weak transcription	K562	blood
41	chr11:77641600-77671000	Weak transcription	Hela-S3	cervix
42	chr11:77642200-77668000	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr11:77644600-77667200	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr11:77644800-77667400	Weak transcription	Spleen	Spleen
45	chr11:77645000-77665000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr11:77645000-77665400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr11:77645000-77666200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr11:77645000-77667200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr11:77645000-77680400	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr11:77645000-77690000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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