Variant report

Variant	rs621456
Chromosome Location	chr11:77553030-77553031
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10899404	0.84[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs11237280	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11237318	0.82[EUR][1000 genomes]
rs11600998	0.82[ASN][1000 genomes]
rs11603438	0.80[ASN][1000 genomes]
rs11604207	1.00[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs11607512	0.83[MEX][hapmap]
rs12285765	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12286317	1.00[CHB][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs17752458	0.83[MEX][hapmap]
rs1783544	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2154972	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs24356	0.84[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2508189	0.82[EUR][1000 genomes]
rs34130561	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3824865	1.00[YRI][hapmap]
rs4322421	0.81[EUR][1000 genomes]
rs4344516	0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap]
rs484363	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4945220	0.84[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs537811	0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs56218634	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs588217	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs598071	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs614495	1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs623173	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs623907	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs635195	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs636971	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs643388	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]
rs648601	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs648896	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs650171	0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs663674	1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs667225	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs668701	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs670090	0.80[EUR][1000 genomes]
rs684813	1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs687037	0.83[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs694845	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs695046	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs7123080	0.84[CEU][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72945598	0.86[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs72947625	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs72947668	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs72949616	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72949618	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7950873	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs7951033	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs947841	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs621456	INTS4	cis	cerebellum	SCAN
rs621456	C11orf67	cis	cerebellum	SCAN
rs621456	INTS4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77533000-77553800	Weak transcription	Brain Angular Gyrus	brain
2	chr11:77533000-77554000	Weak transcription	Brain Substantia Nigra	brain
3	chr11:77533000-77554200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr11:77533400-77553800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr11:77533400-77554000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr11:77533400-77565600	Weak transcription	Gastric	stomach
7	chr11:77533400-77565600	Weak transcription	Pancreas	Pancrea
8	chr11:77534600-77555400	Weak transcription	Lung	lung
9	chr11:77535200-77553800	Weak transcription	NHDF-Ad	bronchial
10	chr11:77535200-77554200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr11:77535200-77554400	Weak transcription	HSMM	muscle
12	chr11:77535400-77553400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr11:77535400-77553400	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr11:77535400-77554200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr11:77535400-77555000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr11:77535400-77565600	Weak transcription	HepG2	liver
17	chr11:77541600-77553800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr11:77544600-77555400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr11:77544600-77564400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr11:77544600-77565400	Weak transcription	Spleen	Spleen
21	chr11:77544800-77553400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr11:77544800-77554200	Weak transcription	Duodenum Mucosa	Duodenum
23	chr11:77544800-77554200	Weak transcription	Dnd41	blood
24	chr11:77544800-77554400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr11:77544800-77564400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr11:77544800-77565400	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr11:77545000-77554000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr11:77545000-77555400	Weak transcription	Fetal Kidney	kidney
29	chr11:77547200-77565800	Weak transcription	Fetal Heart	heart
30	chr11:77547600-77555200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr11:77548800-77582800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr11:77549000-77553400	Weak transcription	NH-A	brain
33	chr11:77550000-77565600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr11:77550200-77553400	Weak transcription	Primary T cells from cord blood	blood
35	chr11:77550200-77554000	Weak transcription	Brain Anterior Caudate	brain
36	chr11:77550400-77554200	Weak transcription	HSMMtube	muscle
37	chr11:77550400-77557200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr11:77550800-77554200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr11:77550800-77564000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr11:77550800-77565400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr11:77551000-77555400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr11:77551200-77558400	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr11:77551400-77565400	Weak transcription	Fetal Thymus	thymus
44	chr11:77551800-77556600	Strong transcription	Ovary	ovary
45	chr11:77552000-77553800	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr11:77552000-77555400	Strong transcription	Fetal Intestine Large	intestine
47	chr11:77552000-77555400	Strong transcription	Fetal Stomach	stomach
48	chr11:77552000-77560400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr11:77552000-77562600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr11:77552200-77554400	Weak transcription	Fetal Brain Female	brain

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