Variant report

Variant	rs1790250
Chromosome Location	chr11:77635315-77635316
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10751278	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10793265	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10899403	0.81[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap]
rs10899405	0.81[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap]
rs10899406	0.81[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap]
rs10899407	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs10899408	0.82[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap]
rs10899409	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs11237295	0.85[CHB][hapmap];0.84[JPT][hapmap]
rs11237339	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11237340	0.95[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1783546	0.81[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap]
rs1790246	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs1793336	0.81[CHB][hapmap]
rs1793343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1823508	0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2034499	0.86[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2276441	0.95[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.80[YRI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2510963	0.84[AMR][1000 genomes]
rs2510967	0.82[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap]
rs3018164	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3018412	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4245453	0.84[JPT][hapmap]
rs584854	0.81[AMR][1000 genomes]
rs597346	0.91[CEU][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs628198	0.89[AMR][1000 genomes]
rs630274	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs630711	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6592747	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6592752	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6592753	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6592756	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs669869	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs672460	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]
rs7110670	0.95[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7127510	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7927913	0.82[CEU][hapmap];0.85[CHB][hapmap];0.84[JPT][hapmap]
rs7931272	0.85[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap]
rs7931392	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7938133	0.95[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7938648	0.90[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7941732	0.95[CEU][hapmap];0.81[CHB][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9988883	0.81[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1790250	INTS4	cis	Muscle Skeletal	GTEx
rs1790250	INTS4	cis	multi-tissue	Pritchard
rs1790250	INTS4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 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	chr11:77591800-77650400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr11:77592800-77690000	Weak transcription	Small Intestine	intestine
5	chr11:77595800-77671000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr11:77597800-77644200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr11:77597800-77644400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr11:77597800-77669800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr11:77597800-77671000	Weak transcription	Fetal Brain Male	brain
10	chr11:77597800-77678200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr11:77597800-77690000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:77597800-77690000	Weak transcription	Esophagus	oesophagus
13	chr11:77597800-77690000	Weak transcription	Gastric	stomach
14	chr11:77602000-77640600	Weak transcription	K562	blood
15	chr11:77602600-77644200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr11:77602800-77690000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr11:77603000-77637400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr11:77603200-77650200	Weak transcription	Fetal Brain Female	brain
19	chr11:77604800-77644200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr11:77612600-77637000	Weak transcription	Brain Anterior Caudate	brain
21	chr11:77614800-77638800	Weak transcription	Brain Angular Gyrus	brain
22	chr11:77614800-77700200	Weak transcription	Psoas Muscle	Psoas
23	chr11:77615000-77644200	Weak transcription	Spleen	Spleen
24	chr11:77615000-77656400	Weak transcription	Right Ventricle	heart
25	chr11:77615200-77637400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr11:77618200-77668200	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr11:77618800-77637200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr11:77618800-77644200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr11:77619000-77636600	Weak transcription	Placenta	Placenta
30	chr11:77619000-77667000	Weak transcription	Fetal Kidney	kidney
31	chr11:77619000-77668000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr11:77619200-77637200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr11:77619200-77637400	Weak transcription	GM12878-XiMat	blood
34	chr11:77620800-77642000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr11:77622200-77635600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr11:77622600-77636800	Weak transcription	Primary B cells from cord blood	blood
37	chr11:77625800-77665600	Weak transcription	HSMMtube	muscle
38	chr11:77625800-77697400	Weak transcription	Rectal Smooth Muscle	rectum
39	chr11:77626000-77635600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr11:77626000-77638000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr11:77626000-77666200	Weak transcription	Brain Substantia Nigra	brain
42	chr11:77626000-77690000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr11:77626200-77641600	Weak transcription	Osteobl	bone
44	chr11:77626200-77665400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr11:77626200-77689400	Weak transcription	Colon Smooth Muscle	Colon
46	chr11:77626600-77636800	Weak transcription	Stomach Smooth Muscle	stomach
47	chr11:77626600-77638800	Weak transcription	Fetal Lung	lung
48	chr11:77626600-77644800	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr11:77626600-77665600	Weak transcription	Ovary	ovary
50	chr11:77626600-77689600	Weak transcription	Rectal Mucosa Donor 31	rectum

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