Variant report

Variant	rs643388
Chromosome Location	chr11:77471042-77471043
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10899394	0.88[TSI][hapmap]
rs10899399	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10899404	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11237244	0.82[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs11237249	1.00[ASW][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap];1.00[YRI][hapmap]
rs11237263	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11237280	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11237318	0.88[EUR][1000 genomes]
rs11600998	0.95[ASN][1000 genomes]
rs11603438	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11604207	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs11606549	0.86[EUR][1000 genomes]
rs12285765	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12286317	0.94[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17752006	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1783544	0.91[EUR][1000 genomes]
rs2032395	0.82[TSI][hapmap]
rs2154972	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs24356	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs2508189	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34130561	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4322421	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4344516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs484363	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4945220	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs537811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56218634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs588217	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs598071	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs614495	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs621456	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs623173	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs623907	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs635195	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs636971	0.93[EUR][1000 genomes]
rs648601	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs648896	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs650171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs663674	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs667225	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs668701	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs670090	0.89[EUR][1000 genomes]
rs684813	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs687037	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs694845	0.93[EUR][1000 genomes]
rs695046	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs7122968	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7123080	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72945592	0.81[EUR][1000 genomes]
rs72945598	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72947625	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72947668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72949616	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72949618	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7950873	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7951033	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs947841	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049603	chr11:76900813-77520411	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv541090	chr11:76900813-77520411	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	nsv976491	chr11:77459085-77487555	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs643388	C11orf67	cis	cerebellum	SCAN
rs643388	INTS4	cis	cerebellum	SCAN
rs643388	INTS4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77409600-77478200	Weak transcription	Brain Angular Gyrus	brain
2	chr11:77410400-77477600	Weak transcription	Brain Substantia Nigra	brain
3	chr11:77431600-77482400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr11:77436200-77473400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr11:77436200-77477000	Weak transcription	Colonic Mucosa	Colon
6	chr11:77436600-77473200	Weak transcription	NHDF-Ad	bronchial
7	chr11:77442400-77472600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr11:77442800-77474600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr11:77442800-77500200	Weak transcription	Pancreas	Pancrea
10	chr11:77443200-77473600	Weak transcription	Fetal Brain Female	brain
11	chr11:77443200-77500200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr11:77445800-77476800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:77446200-77482400	Weak transcription	Spleen	Spleen
14	chr11:77446400-77474800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr11:77448800-77473200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr11:77449800-77474600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr11:77450600-77474600	Weak transcription	Brain Hippocampus Middle	brain
18	chr11:77452000-77479400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr11:77452200-77473400	Weak transcription	Hela-S3	cervix
20	chr11:77452200-77481600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr11:77452600-77474600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr11:77453200-77473200	Weak transcription	Duodenum Mucosa	Duodenum
23	chr11:77459000-77474600	Weak transcription	NHLF	lung
24	chr11:77459200-77472200	Weak transcription	Liver	Liver
25	chr11:77459200-77473200	Weak transcription	HSMM	muscle
26	chr11:77459200-77473400	Weak transcription	HMEC	breast
27	chr11:77459200-77474400	Weak transcription	NH-A	brain
28	chr11:77459400-77498200	Weak transcription	NHEK	skin
29	chr11:77460000-77495800	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr11:77460200-77474600	Weak transcription	HUVEC	blood vessel
31	chr11:77460600-77474600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr11:77462200-77500200	Weak transcription	Gastric	stomach
33	chr11:77462800-77481200	Weak transcription	Right Ventricle	heart
34	chr11:77463600-77477600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr11:77463800-77471200	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr11:77463800-77473200	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr11:77463800-77474600	Weak transcription	Colon Smooth Muscle	Colon
38	chr11:77463800-77527000	Weak transcription	Aorta	Aorta
39	chr11:77464000-77474400	Weak transcription	Brain Anterior Caudate	brain
40	chr11:77464000-77474800	Weak transcription	Lung	lung
41	chr11:77464000-77480600	Weak transcription	Fetal Heart	heart
42	chr11:77464200-77473400	Weak transcription	Rectal Smooth Muscle	rectum
43	chr11:77464400-77476200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr11:77464600-77474600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr11:77464600-77475000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr11:77464600-77475600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr11:77464600-77476200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr11:77464800-77475400	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr11:77464800-77475600	Strong transcription	Dnd41	blood
50	chr11:77465000-77473200	Weak transcription	Left Ventricle	heart

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