Variant report

Variant	rs11631040
Chromosome Location	chr15:49716007-49716008
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10047970	0.86[CEU][hapmap];0.85[TSI][hapmap]
rs10083602	0.81[EUR][1000 genomes]
rs10519230	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1057638	0.80[EUR][1000 genomes]
rs11070692	0.95[YRI][hapmap];0.88[AFR][1000 genomes]
rs11070693	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11070694	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11070696	0.81[CEU][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs11630629	0.89[CEU][hapmap];0.80[AMR][1000 genomes]
rs11631687	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11632674	0.86[CEU][hapmap]
rs11634751	0.86[CEU][hapmap]
rs11636378	0.81[CEU][hapmap]
rs11636671	0.83[ASN][1000 genomes]
rs11636795	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11638378	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11852524	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap]
rs12437460	0.80[EUR][1000 genomes]
rs12438444	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12438856	0.81[EUR][1000 genomes]
rs12439479	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12440323	0.86[CEU][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12441004	0.81[AMR][1000 genomes]
rs12441304	0.86[CEU][hapmap]
rs12442143	0.81[EUR][1000 genomes]
rs12442701	0.80[EUR][1000 genomes]
rs12900001	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12913745	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1429556	0.95[YRI][hapmap];0.87[AFR][1000 genomes]
rs1532955	0.86[CEU][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs1588130	0.86[CEU][hapmap]
rs1605481	0.86[CEU][hapmap]
rs16962243	0.82[CEU][hapmap];0.88[GIH][hapmap]
rs16962486	0.90[AFR][1000 genomes]
rs16962490	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16962528	0.81[EUR][1000 genomes]
rs16973952	0.81[EUR][1000 genomes]
rs17401417	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1874615	0.86[CEU][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs1904317	0.80[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[MEX][hapmap]
rs1911614	0.86[CEU][hapmap];0.85[TSI][hapmap]
rs2413942	0.90[CEU][hapmap];1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs2413946	0.81[EUR][1000 genomes]
rs2413953	0.86[CEU][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs2413954	0.86[CEU][hapmap]
rs2413959	0.86[CEU][hapmap]
rs28460471	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2899433	0.86[CEU][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs4303431	0.86[CEU][hapmap]
rs4316697	0.89[ASW][hapmap];0.92[GIH][hapmap];0.90[LWK][hapmap];0.80[MEX][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes]
rs4321137	0.80[EUR][1000 genomes]
rs4350524	0.86[CEU][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs4614670	0.81[EUR][1000 genomes]
rs4775803	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs4775811	0.80[EUR][1000 genomes]
rs4775814	0.86[CEU][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap]
rs4775815	0.86[CEU][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs520949	0.87[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap]
rs57186766	0.80[EUR][1000 genomes]
rs58284238	0.80[EUR][1000 genomes]
rs58410445	0.81[EUR][1000 genomes]
rs6493364	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs6493369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6493371	0.86[CEU][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs6493376	0.86[CEU][hapmap]
rs7162800	0.87[MEX][hapmap]
rs7166049	0.81[EUR][1000 genomes]
rs7166202	0.86[CEU][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs7166498	0.86[CEU][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs7167041	0.86[CEU][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs7167429	0.86[CEU][hapmap]
rs7170426	0.86[CEU][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs7178143	0.86[CEU][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs7178468	0.86[CEU][hapmap]
rs733097	0.86[CEU][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap]
rs8026236	0.81[EUR][1000 genomes]
rs8031892	0.88[AFR][1000 genomes]
rs8032650	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap]
rs8035468	0.86[CEU][hapmap]
rs8039062	0.80[EUR][1000 genomes]
rs8041781	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs965134	0.86[CEU][hapmap]
rs9920772	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9972329	0.86[CEU][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs9972429	0.81[EUR][1000 genomes]
rs9972565	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039368	chr15:49566094-49764066	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833002	chr15:49621400-49781799	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11631040	GALK2	Cis_1M	lymphoblastoid	RTeQTL
rs11631040	CATSPER2P1	cis	cerebellum	SCAN
rs11631040	DTWD1	cis	lymphoblastoid	seeQTL
rs11631040	DTWD1	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:49714000-49720400	Active TSS	Ovary	ovary
2	chr15:49714000-49720800	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr15:49714000-49721000	Active TSS	Colon Smooth Muscle	Colon
4	chr15:49714000-49722600	Active TSS	Stomach Smooth Muscle	stomach
5	chr15:49714200-49716400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr15:49714200-49716800	Active TSS	Skeletal Muscle Male	skeletal muscle
7	chr15:49714200-49718600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr15:49714200-49719400	Active TSS	Fetal Kidney	kidney
9	chr15:49714200-49721000	Active TSS	Rectal Smooth Muscle	rectum
10	chr15:49714200-49721000	Active TSS	Right Atrium	heart
11	chr15:49714200-49721400	Active TSS	Adipose Nuclei	Adipose
12	chr15:49714400-49716600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr15:49714800-49716400	Weak transcription	Brain Substantia Nigra	brain
14	chr15:49714800-49720600	Active TSS	NHDF-Ad	bronchial
15	chr15:49715000-49716200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr15:49715200-49716800	Active TSS	Psoas Muscle	Psoas
17	chr15:49715200-49717600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr15:49715200-49718000	Active TSS	Fetal Muscle Trunk	muscle
19	chr15:49715200-49718000	Active TSS	HSMMtube	muscle
20	chr15:49715200-49719200	Active TSS	Rectal Mucosa Donor 29	rectum
21	chr15:49715200-49719400	Active TSS	Fetal Muscle Leg	muscle
22	chr15:49715200-49719400	Active TSS	Right Ventricle	heart
23	chr15:49715200-49719600	Active TSS	Osteobl	bone
24	chr15:49715200-49720000	Active TSS	Fetal Stomach	stomach
25	chr15:49715400-49716800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr15:49715400-49716800	Enhancers	Brain Cingulate Gyrus	brain
27	chr15:49715400-49716800	Enhancers	Brain Hippocampus Middle	brain
28	chr15:49715400-49716800	ZNF genes & repeats	Fetal Brain Male	brain
29	chr15:49715400-49717600	Active TSS	Fetal Intestine Large	intestine
30	chr15:49715400-49718000	Active TSS	Rectal Mucosa Donor 31	rectum
31	chr15:49715400-49718400	Active TSS	Fetal Intestine Small	intestine
32	chr15:49715400-49721600	Active TSS	NHLF	lung
33	chr15:49715600-49716400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr15:49715600-49716800	Active TSS	Colonic Mucosa	Colon
35	chr15:49715800-49717000	Active TSS	Skeletal Muscle Female	skeletal muscle
36	chr15:49715800-49717400	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr15:49715800-49718000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr15:49716000-49716200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr15:49716000-49716200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr15:49716000-49716400	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr15:49716000-49717600	Active TSS	Fetal Heart	heart
42	chr15:49716000-49718000	Active TSS	Fetal Lung	lung

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