Variant report

Variant	rs1793343
Chromosome Location	chr11:77615613-77615614
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10751278	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10793265	0.82[EUR][1000 genomes]
rs10899403	0.89[ASW][hapmap];0.81[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.84[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap]
rs10899405	0.89[ASW][hapmap];0.81[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap]
rs10899406	0.89[ASW][hapmap];0.81[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs10899407	0.87[CHB][hapmap];0.90[JPT][hapmap]
rs10899408	0.81[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap]
rs10899409	0.89[ASW][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.84[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap]
rs11237295	0.89[ASW][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap]
rs11237340	0.95[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.91[YRI][hapmap];0.81[EUR][1000 genomes]
rs11237348	0.81[CHD][hapmap]
rs1783546	0.89[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.85[ASN][1000 genomes]
rs1790235	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1790240	0.82[ASN][1000 genomes]
rs1790246	0.89[ASW][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap]
rs1790250	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]
rs1790253	0.82[AMR][1000 genomes]
rs1793334	0.85[ASN][1000 genomes]
rs1793336	0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs1793341	0.83[ASN][1000 genomes]
rs1823508	0.81[YRI][hapmap];0.80[EUR][1000 genomes]
rs2034499	0.89[ASW][hapmap];0.86[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs2276441	0.95[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap]
rs2510967	0.81[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs3018164	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3018412	0.81[EUR][1000 genomes]
rs3018415	0.88[ASN][1000 genomes]
rs4245453	0.82[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap]
rs496786	0.89[ASW][hapmap];0.86[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap]
rs597346	0.91[CEU][hapmap];1.00[YRI][hapmap]
rs628198	0.80[AMR][1000 genomes]
rs630274	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs630711	0.95[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs6592752	0.81[EUR][1000 genomes]
rs6592753	0.81[EUR][1000 genomes]
rs672460	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]
rs7110670	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs7127510	0.82[EUR][1000 genomes]
rs7927913	0.81[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap]
rs7931272	0.84[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap]
rs7938133	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap]
rs7938648	0.90[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes]
rs7941732	0.95[CEU][hapmap]
rs9988883	0.89[ASW][hapmap];0.81[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.90[MEX][hapmap];0.93[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	nsv555453	chr11:77577494-77618441	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv975954	chr11:77600915-77617903	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1793343	INTS4	cis	multi-tissue	Pritchard
rs1793343	INTS4	cis	cerebellum	SCAN
rs1793343	PAK1	cis	cerebellum	SCAN
rs1793343	INTS4	Cis_1M	lymphoblastoid	RTeQTL
rs1793343	INT4	cis	multi-tissue	Pritchard
rs1793343	INTS4	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77577400-77630800	Weak transcription	Fetal Heart	heart
2	chr11:77579200-77625000	Weak transcription	HMEC	breast
3	chr11:77583400-77670600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr11:77583400-77690000	Weak transcription	Colonic Mucosa	Colon
5	chr11:77586600-77625000	Weak transcription	Stomach Mucosa	stomach
6	chr11:77587200-77617600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr11:77591800-77650400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr11:77592800-77690000	Weak transcription	Small Intestine	intestine
9	chr11:77593800-77625000	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr11:77595400-77620000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr11:77595800-77671000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr11:77597400-77617400	Weak transcription	Brain Hippocampus Middle	brain
13	chr11:77597400-77625000	Weak transcription	A549	lung
14	chr11:77597600-77617400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr11:77597600-77629400	Weak transcription	Brain Germinal Matrix	brain
16	chr11:77597800-77617400	Weak transcription	GM12878-XiMat	blood
17	chr11:77597800-77617600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr11:77597800-77617600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr11:77597800-77617800	Weak transcription	Fetal Kidney	kidney
20	chr11:77597800-77620000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr11:77597800-77624800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr11:77597800-77625000	Weak transcription	Colon Smooth Muscle	Colon
23	chr11:77597800-77625000	Weak transcription	Pancreas	Pancrea
24	chr11:77597800-77625000	Weak transcription	NHDF-Ad	bronchial
25	chr11:77597800-77625200	Weak transcription	NHEK	skin
26	chr11:77597800-77625600	Weak transcription	HSMM	muscle
27	chr11:77597800-77629000	Weak transcription	Aorta	Aorta
28	chr11:77597800-77633800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr11:77597800-77644200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr11:77597800-77644400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr11:77597800-77669800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr11:77597800-77671000	Weak transcription	Fetal Brain Male	brain
33	chr11:77597800-77678200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr11:77597800-77690000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr11:77597800-77690000	Weak transcription	Esophagus	oesophagus
36	chr11:77597800-77690000	Weak transcription	Gastric	stomach
37	chr11:77601000-77618000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr11:77601800-77617400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr11:77601800-77629800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr11:77602000-77640600	Weak transcription	K562	blood
41	chr11:77602200-77617800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr11:77602600-77625200	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr11:77602600-77644200	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr11:77602800-77690000	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr11:77603000-77625000	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr11:77603000-77637400	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr11:77603200-77618000	Weak transcription	Brain Substantia Nigra	brain
48	chr11:77603200-77622200	Weak transcription	NH-A	brain
49	chr11:77603200-77625000	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr11:77603200-77625000	Weak transcription	Osteobl	bone

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