Variant report

Variant	rs4150650
Chromosome Location	chr11:18374279-18374280
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10734259	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10741741	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10741742	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10832917	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10832921	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11024634	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1140047	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12286683	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12293544	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1520884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2061164	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2124374	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3740711	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3802968	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3825025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4150526	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4150550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4150562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4150566	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150579	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];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150588	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150609	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4150610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4150612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150615	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4150641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4150642	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4150651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150653	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4150655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4150673	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];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4353250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4757637	1.00[CHB][hapmap]
rs4757645	0.86[CEU][hapmap]
rs6486419	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7103375	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7129995	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7947378	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9783347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9988866	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];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[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	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats 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 miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv933836	chr11:18300254-18440933	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv553633	chr11:18311701-19058451	Weak transcription Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
4	nsv1047049	chr11:18359702-18520008	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv540955	chr11:18359702-18520008	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs4150650	PIK3C2A	cis	cerebellum	SCAN
rs4150650	GTF2H1	cis	lymphoblastoid	seeQTL
rs4150650	GTF2H1	cis	parietal	SCAN
rs4150650	GTF2H1	cis	Stomach	GTEx
rs4150650	LDHA	cis	parietal	SCAN
rs4150650	ABCC8	cis	parietal	SCAN
rs4150650	GTF2H1	cis	Esophagus Mucosa	GTEx
rs4150650	GTF2H1	cis	cerebellum	SCAN
rs4150650	GTF2H1	cis	Esophagus Muscularis	GTEx
rs4150650	HPS5	cis	cerebellum	SCAN
rs4150650	NELL1	cis	parietal	SCAN
rs4150650	LDHAL6A	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18345000-18383200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:18345000-18405000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:18346800-18382800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr11:18346800-18390400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr11:18347000-18387400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr11:18351200-18387000	Weak transcription	Stomach Mucosa	stomach
7	chr11:18352400-18389000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr11:18354400-18389400	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr11:18357000-18389200	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr11:18357200-18379600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr11:18360000-18382200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr11:18360200-18374400	Weak transcription	Small Intestine	intestine
13	chr11:18361800-18391600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr11:18362400-18374400	Weak transcription	Aorta	Aorta
15	chr11:18363000-18390200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr11:18363200-18379400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr11:18363200-18393000	Weak transcription	Fetal Heart	heart
18	chr11:18365800-18381400	Weak transcription	Pancreas	Pancrea
19	chr11:18366600-18381400	Weak transcription	Gastric	stomach
20	chr11:18367200-18375400	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr11:18367600-18390000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr11:18368000-18376000	Weak transcription	Right Ventricle	heart
23	chr11:18368000-18382400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr11:18368200-18375400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr11:18368200-18379400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr11:18368200-18379800	Weak transcription	Fetal Brain Male	brain
27	chr11:18368600-18381400	Weak transcription	Spleen	Spleen
28	chr11:18369600-18374800	Weak transcription	Esophagus	oesophagus
29	chr11:18369600-18379600	Weak transcription	Colon Smooth Muscle	Colon
30	chr11:18369600-18385800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr11:18369800-18374600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr11:18369800-18377000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr11:18369800-18379600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr11:18369800-18380600	Weak transcription	NHLF	lung
35	chr11:18370000-18374800	Weak transcription	Brain Anterior Caudate	brain
36	chr11:18370000-18375000	Weak transcription	GM12878-XiMat	blood
37	chr11:18370000-18377400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr11:18370000-18378600	Weak transcription	HepG2	liver
39	chr11:18370000-18379200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr11:18370000-18379200	Weak transcription	Rectal Smooth Muscle	rectum
41	chr11:18370200-18374800	Weak transcription	Colonic Mucosa	Colon
42	chr11:18370200-18379800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr11:18370400-18374800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr11:18370400-18377400	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr11:18370400-18380000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr11:18370600-18375000	Weak transcription	Brain Angular Gyrus	brain
47	chr11:18370600-18375200	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr11:18370600-18379800	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr11:18371200-18374400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr11:18371200-18374400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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