Variant report

Variant	rs36036499
Chromosome Location	chr11:57494198-57494199
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:57489018..57490635-chr11:57493896..57496421,2	K562	blood:
2	chr11:57493357..57495761-chr11:57498560..57501047,2	MCF-7	breast:

Extended variants
information (count: 87 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10750870	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10792110	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10896644	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10896649	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10896653	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11229109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11229119	0.82[AMR][1000 genomes]
rs11570176	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11570181	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12270209	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12274865	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12363024	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12801694	0.84[ASW][hapmap];0.85[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs12805343	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1424753	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1613592	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[ASN][1000 genomes]
rs1624389	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1631684	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1647394	0.82[ASN][1000 genomes]
rs1647403	0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs17455422	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17455626	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1783818	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1783824	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1783826	1.00[JPT][hapmap]
rs1783827	1.00[JPT][hapmap]
rs1783828	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs1783976	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1783977	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1783978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1783979	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1783980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1783981	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1783983	0.89[CEU][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs1783985	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1785498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1785499	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1786438	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1798172	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[ASN][1000 genomes]
rs1798173	0.84[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[ASN][1000 genomes]
rs1798177	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs2156638	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2911728	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2956981	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2956982	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3017889	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4611222	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs471398	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs547118	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56392705	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs585337	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs585761	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs588612	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs593239	0.81[ASN][1000 genomes]
rs606499	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs615133	0.85[ASW][hapmap];0.81[LWK][hapmap];0.82[MEX][hapmap];0.83[YRI][hapmap]
rs623541	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs627145	0.88[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs633129	0.85[ASW][hapmap];0.82[MEX][hapmap];0.83[YRI][hapmap]
rs639158	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs644219	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs645145	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs652191	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs652908	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs653889	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs658936	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs659165	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs665058	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs666021	0.84[JPT][hapmap]
rs671508	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs682258	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs686489	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7105506	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7115528	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7117020	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7120868	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7479922	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7947357	1.00[JPT][hapmap]
rs7948571	0.93[ASN][1000 genomes]
rs929934	1.00[JPT][hapmap]

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	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv832164	chr11:57407617-57578825	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv508633	chr11:57419585-57560045	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	nsv975188	chr11:57480320-57494198	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs36036499	TIMM10	cis	parietal	SCAN
rs36036499	MS4A7	cis	parietal	SCAN
rs36036499	SMTNL1	cis	lymphoblastoid	seeQTL
rs36036499	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs36036499	SLC43A3	cis	cerebellum	SCAN
rs36036499	YPEL4	cis	lung	GTEx
rs36036499	TNKS1BP1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57481000-57496200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:57481000-57508400	Weak transcription	Aorta	Aorta
3	chr11:57481200-57508400	Weak transcription	Fetal Brain Male	brain
4	chr11:57481400-57496400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr11:57481400-57500200	Weak transcription	Esophagus	oesophagus
6	chr11:57481400-57503200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr11:57481400-57505000	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr11:57481400-57506000	Weak transcription	Pancreas	Pancrea
9	chr11:57481600-57505000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr11:57481600-57505000	Weak transcription	Fetal Kidney	kidney
11	chr11:57481600-57505000	Weak transcription	NH-A	brain
12	chr11:57481600-57506200	Weak transcription	Colonic Mucosa	Colon
13	chr11:57481600-57508400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr11:57481800-57496000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr11:57481800-57503000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr11:57481800-57503000	Weak transcription	HSMM	muscle
17	chr11:57481800-57505000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr11:57481800-57505000	Weak transcription	Fetal Lung	lung
19	chr11:57482000-57505000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr11:57482000-57505000	Weak transcription	NHLF	lung
21	chr11:57482000-57505200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr11:57482000-57505200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr11:57482000-57508200	Weak transcription	Brain Substantia Nigra	brain
24	chr11:57482200-57495200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr11:57482200-57496000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr11:57482200-57496400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr11:57482200-57498000	Weak transcription	HUVEC	blood vessel
28	chr11:57482200-57505000	Weak transcription	Brain Anterior Caudate	brain
29	chr11:57482200-57505000	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr11:57482200-57505200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr11:57482200-57508200	Weak transcription	Colon Smooth Muscle	Colon
32	chr11:57482400-57494200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr11:57482400-57496000	Weak transcription	Brain Hippocampus Middle	brain
34	chr11:57482400-57500400	Weak transcription	Hela-S3	cervix
35	chr11:57482400-57503000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr11:57482400-57504800	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr11:57482400-57505000	Weak transcription	Brain Angular Gyrus	brain
38	chr11:57482400-57508000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr11:57482400-57508200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr11:57482400-57508200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr11:57482400-57508200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr11:57482600-57499800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr11:57482600-57503000	Weak transcription	Fetal Heart	heart
44	chr11:57482600-57508000	Weak transcription	Small Intestine	intestine
45	chr11:57482800-57499600	Weak transcription	Psoas Muscle	Psoas
46	chr11:57485000-57495000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr11:57486000-57496200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr11:57486000-57502000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr11:57486000-57502800	Weak transcription	Right Ventricle	heart
50	chr11:57486000-57504800	Weak transcription	Primary B cells from cord blood	blood

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