Variant report

Variant	rs7938648
Chromosome Location	chr11:77682882-77682883
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:77680388..77683002-chr11:77686892..77688723,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10751278	0.86[EUR][1000 genomes]
rs10793265	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10899407	0.81[JPT][hapmap]
rs10899408	0.81[CEU][hapmap];0.81[CHB][hapmap]
rs10899409	0.85[CHB][hapmap]
rs11237339	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11237340	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11237348	1.00[YRI][hapmap]
rs1783546	0.80[CEU][hapmap];0.90[CHB][hapmap]
rs1790246	0.85[CHB][hapmap]
rs1790250	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]
rs1793343	0.90[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes]
rs1823508	0.81[CEU][hapmap];0.80[CHB][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2034499	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276441	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2510967	0.81[CEU][hapmap];0.81[CHB][hapmap]
rs3018164	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3018412	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs597346	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs628198	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs630274	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs630711	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6592747	0.90[EUR][1000 genomes]
rs6592752	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6592753	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6592756	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs669869	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs672460	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]
rs7110670	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7127510	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7931392	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7938133	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7941732	0.95[CEU][hapmap];0.88[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9988883	0.80[CEU][hapmap];0.85[CHB][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	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7938648	INTS4	cis	multi-tissue	Pritchard
rs7938648	INTS4	cis	Muscle Skeletal	GTEx
rs7938648	INTS4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77583400-77690000	Weak transcription	Colonic Mucosa	Colon
2	chr11:77592800-77690000	Weak transcription	Small Intestine	intestine
3	chr11:77597800-77690000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:77597800-77690000	Weak transcription	Esophagus	oesophagus
5	chr11:77597800-77690000	Weak transcription	Gastric	stomach
6	chr11:77602800-77690000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr11:77614800-77700200	Weak transcription	Psoas Muscle	Psoas
8	chr11:77625800-77697400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr11:77626000-77690000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr11:77626200-77689400	Weak transcription	Colon Smooth Muscle	Colon
11	chr11:77626600-77689600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr11:77626600-77690000	Weak transcription	Pancreas	Pancrea
13	chr11:77627800-77684800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr11:77645000-77690000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr11:77646200-77689600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr11:77648600-77690000	Weak transcription	Brain Germinal Matrix	brain
17	chr11:77649200-77701200	Weak transcription	NH-A	brain
18	chr11:77655400-77684400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr11:77658600-77689200	Weak transcription	HUVEC	blood vessel
20	chr11:77661400-77704400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr11:77664200-77689400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr11:77664200-77704000	Weak transcription	NHEK	skin
23	chr11:77665800-77689400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr11:77665800-77704200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr11:77666000-77704400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr11:77667600-77684800	Weak transcription	Fetal Kidney	kidney
27	chr11:77667600-77704200	Weak transcription	NHLF	lung
28	chr11:77668400-77689600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr11:77668400-77701200	Weak transcription	Aorta	Aorta
30	chr11:77668600-77690000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr11:77668600-77690000	Weak transcription	Lung	lung
32	chr11:77670000-77690000	Weak transcription	Spleen	Spleen
33	chr11:77670200-77689800	Weak transcription	HMEC	breast
34	chr11:77671000-77689800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr11:77671200-77704200	Weak transcription	NHDF-Ad	bronchial
36	chr11:77671400-77684400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr11:77671400-77688800	Weak transcription	Left Ventricle	heart
38	chr11:77671800-77689600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr11:77671800-77689800	Weak transcription	Brain Angular Gyrus	brain
40	chr11:77672000-77684600	Weak transcription	A549	lung
41	chr11:77672000-77684800	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr11:77672000-77685600	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr11:77672000-77689400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr11:77672000-77689600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr11:77672000-77689600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr11:77672000-77689800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr11:77672000-77689800	Weak transcription	HepG2	liver
48	chr11:77672000-77690400	Weak transcription	Hela-S3	cervix
49	chr11:77672000-77701200	Weak transcription	Brain Cingulate Gyrus	brain
50	chr11:77672000-77703800	Weak transcription	Fetal Brain Male	brain

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