Variant report

Variant	rs4539328
Chromosome Location	chr11:120218243-120218244
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	chr11:120218082..120220509-chr11:120283628..120285454,2	K562	blood:
2	chr11:120212208..120214300-chr11:120217679..120220181,2	MCF-7	breast:

Extended variants
information (count: 88 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10502235	0.90[JPT][hapmap]
rs10750172	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10750173	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10750174	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10790378	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10790380	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10790382	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10790383	0.92[CEU][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs10892562	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10892563	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10892564	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10892566	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10892567	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10892570	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10892574	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10892576	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10892578	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11217821	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11217840	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11217841	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11217852	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11217874	0.84[JPT][hapmap]
rs11217875	0.89[JPT][hapmap]
rs11600703	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11601535	0.83[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[EUR][1000 genomes]
rs11823300	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11827818	0.84[JPT][hapmap]
rs12361632	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12417581	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12420378	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12787285	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12806740	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1892894	0.92[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1893261	0.96[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2276035	0.84[JPT][hapmap]
rs2305008	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs2305010	0.88[ASW][hapmap];0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.81[EUR][1000 genomes]
rs34298380	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36011588	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3809059	0.81[JPT][hapmap]
rs4381380	0.92[CEU][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4936517	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4938799	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4938801	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4938804	0.92[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4938805	0.88[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4938806	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4938807	0.90[JPT][hapmap]
rs4938808	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs496248	0.81[JPT][hapmap]
rs61898351	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs632137	0.81[JPT][hapmap]
rs6589810	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6589811	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6589812	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6589813	0.84[EUR][1000 genomes]
rs7101415	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7104639	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7107211	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7115714	0.82[EUR][1000 genomes]
rs7117063	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7117321	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7118391	0.98[GIH][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7121779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7126328	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7126413	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7129944	0.90[JPT][hapmap]
rs7131046	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7131597	0.92[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes]
rs723937	0.92[CEU][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7478880	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7924772	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7924963	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7924975	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7932037	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7932658	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7933086	0.92[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7937612	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7939137	0.92[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs7948928	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7951250	0.81[AMR][1000 genomes]
rs7952529	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs894839	0.82[ASW][hapmap];0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.80[EUR][1000 genomes]
rs9633919	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9633950	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054057	chr11:119781953-120519770	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv541178	chr11:119781953-120519770	Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv529003	chr11:120209386-120355230	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4539328	TMEM136	cis	parietal	SCAN
rs4539328	ARHGEF12	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120208800-120223400	Weak transcription	Gastric	stomach
2	chr11:120209600-120224600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr11:120211000-120218600	Enhancers	Fetal Heart	heart
4	chr11:120211000-120224400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr11:120211200-120218600	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr11:120211600-120219000	Enhancers	Muscle Satellite Cultured Cells	--
7	chr11:120211600-120224400	Weak transcription	A549	lung
8	chr11:120213800-120224600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr11:120214000-120218600	Enhancers	Adipose Nuclei	Adipose
10	chr11:120215000-120223400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr11:120215000-120224400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr11:120215400-120220200	Weak transcription	Right Atrium	heart
13	chr11:120215400-120225600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr11:120215800-120223400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr11:120216000-120224200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr11:120216000-120224800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr11:120216000-120239000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr11:120216200-120223600	Weak transcription	Small Intestine	intestine
19	chr11:120216200-120224600	Weak transcription	Spleen	Spleen
20	chr11:120216200-120224600	Weak transcription	NHEK	skin
21	chr11:120216400-120244800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr11:120216600-120218600	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr11:120216600-120220400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr11:120216800-120218400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr11:120216800-120218400	Enhancers	Fetal Intestine Large	intestine
26	chr11:120216800-120218400	Enhancers	Pancreatic Islets	Pancreatic Islet
27	chr11:120216800-120218600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr11:120216800-120218600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr11:120216800-120218600	Enhancers	HUVEC	blood vessel
30	chr11:120217000-120218400	Enhancers	Duodenum Mucosa	Duodenum
31	chr11:120217000-120218400	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr11:120217000-120218400	Enhancers	Fetal Brain Male	brain
33	chr11:120217000-120218600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr11:120217000-120218600	Enhancers	Fetal Intestine Small	intestine
35	chr11:120217000-120218600	Enhancers	Fetal Kidney	kidney
36	chr11:120217000-120218600	Enhancers	Fetal Lung	lung
37	chr11:120217000-120218600	Enhancers	Fetal Stomach	stomach
38	chr11:120217000-120218600	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr11:120217000-120218600	Enhancers	NHDF-Ad	bronchial
40	chr11:120217000-120218800	Enhancers	Osteobl	bone
41	chr11:120217000-120219200	Enhancers	Brain Anterior Caudate	brain
42	chr11:120217200-120219000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr11:120217200-120219800	Weak transcription	HSMMtube	muscle
44	chr11:120217200-120223400	Weak transcription	Right Ventricle	heart
45	chr11:120217200-120224400	Weak transcription	Lung	lung
46	chr11:120217200-120228600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr11:120217200-120232000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr11:120217400-120218600	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr11:120217400-120219200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr11:120217400-120220200	Weak transcription	K562	blood

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