Variant report

Variant	rs522015
Chromosome Location	chr11:77047515-77047516
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 110 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs11237123	1.00[JPT][hapmap]
rs11237141	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11237142	0.91[ASN][1000 genomes]
rs11237148	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11237150	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11237151	0.91[ASN][1000 genomes]
rs11237160	0.80[AMR][1000 genomes]
rs11237162	0.87[AMR][1000 genomes]
rs11237164	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1125619	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11512967	0.83[ASN][1000 genomes]
rs1225478	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12361757	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12363707	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12363842	0.91[ASN][1000 genomes]
rs12363944	1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.88[MKK][hapmap];0.83[TSI][hapmap]
rs12366261	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.88[ASN][1000 genomes]
rs1237490	0.91[EUR][1000 genomes]
rs12794253	0.91[ASN][1000 genomes]
rs1377472	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1597954	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1622364	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1670446	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1670449	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1670450	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1670456	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1670458	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1670461	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1670462	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17824184	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.91[ASN][1000 genomes]
rs1793468	0.91[ASN][1000 genomes]
rs1793471	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1793472	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1793487	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1793490	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2154754	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs2156567	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2602476	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2602483	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2602487	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2725820	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2725822	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2725825	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2725828	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3015982	0.94[EUR][1000 genomes]
rs3015983	0.92[EUR][1000 genomes]
rs3015985	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs3015986	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3015988	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3015990	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3015992	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs3019233	0.93[EUR][1000 genomes]
rs3019234	0.93[EUR][1000 genomes]
rs3019235	0.92[EUR][1000 genomes]
rs3019236	0.93[EUR][1000 genomes]
rs3019249	0.85[EUR][1000 genomes]
rs3019257	0.92[EUR][1000 genomes]
rs34025917	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34880271	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4375461	0.91[ASN][1000 genomes]
rs472691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs476258	0.89[EUR][1000 genomes]
rs479104	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs493256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs494289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4945150	1.00[JPT][hapmap]
rs503406	0.94[EUR][1000 genomes]
rs505841	0.89[EUR][1000 genomes]
rs508662	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs51500	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs520938	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs523481	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs531638	0.88[EUR][1000 genomes]
rs535008	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs552323	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs557484	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs558470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs560571	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs561386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs562845	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs563731	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs572485	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs576220	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs580624	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs592602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs595654	0.88[EUR][1000 genomes]
rs598801	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs644551	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs649040	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs653792	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs657269	0.81[EUR][1000 genomes]
rs66518011	0.88[ASN][1000 genomes]
rs66540426	0.91[ASN][1000 genomes]
rs66728428	0.91[ASN][1000 genomes]
rs674259	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs683455	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs683762	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs684793	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs686068	1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689108	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7118943	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7934230	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs7949721	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs883224	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs883680	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048360	chr11:76900813-77387933	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv541089	chr11:76900813-77387933	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats 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	24 gene(s)	inside rSNPs	diseases
3	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
4	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
5	esv3424135	chr11:76961603-77277087	Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs522015	KCTD14	cis	cerebellum	SCAN
rs522015	DNAJB13	cis	parietal	SCAN
rs522015	KCTD14	cis	parietal	SCAN
rs522015	PAK1	cis	parietal	SCAN
rs522015	RSF1	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77028000-77068400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr11:77028200-77066000	Weak transcription	Fetal Kidney	kidney
3	chr11:77030600-77086800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr11:77030800-77054200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr11:77031600-77066400	Weak transcription	Gastric	stomach
6	chr11:77031600-77073800	Weak transcription	Spleen	Spleen
7	chr11:77031800-77070400	Weak transcription	Fetal Brain Male	brain
8	chr11:77032200-77066400	Weak transcription	Lung	lung
9	chr11:77033400-77067200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr11:77033400-77090400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr11:77033800-77059200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr11:77034400-77054600	Weak transcription	Pancreas	Pancrea
13	chr11:77034400-77059200	Weak transcription	Psoas Muscle	Psoas
14	chr11:77034400-77086200	Weak transcription	NHLF	lung
15	chr11:77034600-77051600	Weak transcription	Brain Anterior Caudate	brain
16	chr11:77034800-77063800	Weak transcription	Brain Substantia Nigra	brain
17	chr11:77034800-77064000	Weak transcription	Brain Hippocampus Middle	brain
18	chr11:77037600-77051600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr11:77041800-77056600	Weak transcription	HSMMtube	muscle
20	chr11:77042600-77047800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr11:77042600-77048600	Strong transcription	Fetal Muscle Leg	muscle
22	chr11:77042600-77049200	Strong transcription	Duodenum Mucosa	Duodenum
23	chr11:77042600-77053600	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr11:77042800-77048600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr11:77042800-77080800	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr11:77043000-77048000	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr11:77043000-77048600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr11:77043000-77048600	Strong transcription	Fetal Intestine Large	intestine
29	chr11:77043000-77048600	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr11:77043000-77048800	Strong transcription	Primary T cells from cord blood	blood
31	chr11:77043000-77048800	Strong transcription	Stomach Smooth Muscle	stomach
32	chr11:77043000-77049200	Strong transcription	Placenta	Placenta
33	chr11:77043000-77049800	Strong transcription	Adipose Nuclei	Adipose
34	chr11:77043000-77051600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr11:77043000-77056200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr11:77043000-77061000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr11:77043200-77048600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr11:77043200-77048600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr11:77043200-77055400	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr11:77043400-77048400	Strong transcription	Fetal Thymus	thymus
41	chr11:77043400-77048400	Strong transcription	Dnd41	blood
42	chr11:77043400-77054600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr11:77043400-77056800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr11:77043400-77066400	Weak transcription	Esophagus	oesophagus
45	chr11:77043400-77072600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr11:77043400-77074800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr11:77043400-77082400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr11:77043400-77083600	Weak transcription	Thymus	Thymus
49	chr11:77043600-77060800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr11:77043800-77049800	Strong transcription	iPS-15b Cell Line	embryonic stem cell

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