Variant report

Variant	rs4938802
Chromosome Location	chr11:120228989-120228990
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:120227696..120230495-chr11:120243268..120245330,2	K562	blood:
2	chr11:120227977..120230527-chr11:120258363..120260160,2	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10502235	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10750173	0.90[JPT][hapmap]
rs10790381	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10790383	0.90[JPT][hapmap]
rs10892563	0.91[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap]
rs10892565	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10892566	0.90[JPT][hapmap]
rs10892569	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10892575	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11217821	0.90[JPT][hapmap]
rs11217843	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11217857	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11217866	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11217874	0.87[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11217875	0.81[ASW][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11217878	0.84[EUR][1000 genomes]
rs11601535	0.88[JPT][hapmap]
rs11823264	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11823300	0.84[ASN][1000 genomes]
rs11824032	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11827818	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12270397	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12361632	0.90[ASN][1000 genomes]
rs12785387	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12794618	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12806740	0.90[JPT][hapmap]
rs12807097	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17123861	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1812974	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1892894	0.90[JPT][hapmap]
rs1893261	0.90[JPT][hapmap]
rs2276035	1.00[ASW][hapmap];0.88[CEU][hapmap];0.83[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs2305008	0.90[JPT][hapmap]
rs2305010	0.90[JPT][hapmap]
rs4381380	0.83[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4936517	0.99[ASN][1000 genomes]
rs4936518	0.84[ASN][1000 genomes]
rs4938799	0.90[JPT][hapmap]
rs4938803	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4938804	0.89[JPT][hapmap]
rs4938805	0.90[JPT][hapmap]
rs4938806	0.86[ASN][1000 genomes]
rs4938807	0.81[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs4938808	0.90[JPT][hapmap]
rs56693116	0.85[EUR][1000 genomes]
rs6589810	0.86[ASN][1000 genomes]
rs6589812	0.90[JPT][hapmap]
rs6589813	0.84[ASN][1000 genomes]
rs7101415	0.86[ASN][1000 genomes]
rs7115714	0.83[ASN][1000 genomes]
rs7121779	0.90[JPT][hapmap]
rs7129944	1.00[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7131597	0.90[JPT][hapmap]
rs723937	0.89[JPT][hapmap]
rs7924772	0.83[ASN][1000 genomes]
rs7933086	0.90[JPT][hapmap]
rs7939137	0.90[JPT][hapmap]
rs7948928	0.90[JPT][hapmap]
rs894839	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv1050935	chr11:120224544-120276373	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4938802	TMEM136	cis	parietal	SCAN
rs4938802	ARHGEF12	cis	cerebellum	SCAN
rs4938802	SIDT2	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120216000-120239000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr11:120216400-120244800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr11:120217200-120232000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:120217400-120234000	Weak transcription	Aorta	Aorta
5	chr11:120217600-120257000	Weak transcription	HSMM	muscle
6	chr11:120218200-120229600	Weak transcription	GM12878-XiMat	blood
7	chr11:120218600-120231800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr11:120218600-120232000	Weak transcription	Fetal Stomach	stomach
9	chr11:120218600-120232400	Weak transcription	HUVEC	blood vessel
10	chr11:120218800-120230600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr11:120220400-120232800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr11:120220600-120232000	Weak transcription	Colon Smooth Muscle	Colon
13	chr11:120224400-120229400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr11:120224400-120232200	Weak transcription	Fetal Heart	heart
15	chr11:120224800-120231400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr11:120224800-120248800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr11:120224800-120260800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr11:120225000-120229600	Weak transcription	Esophagus	oesophagus
19	chr11:120225000-120229600	Weak transcription	K562	blood
20	chr11:120225000-120248200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr11:120225200-120229400	Weak transcription	Pancreas	Pancrea
22	chr11:120225200-120231800	Weak transcription	Gastric	stomach
23	chr11:120225200-120233800	Weak transcription	NHEK	skin
24	chr11:120225200-120234400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr11:120225200-120242200	Weak transcription	A549	lung
26	chr11:120225200-120251000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr11:120225400-120231800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr11:120225800-120229400	Weak transcription	Left Ventricle	heart
29	chr11:120225800-120229400	Weak transcription	Stomach Smooth Muscle	stomach
30	chr11:120225800-120231800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr11:120225800-120232000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr11:120225800-120232200	Weak transcription	Osteobl	bone
33	chr11:120225800-120242200	Weak transcription	Fetal Intestine Small	intestine
34	chr11:120226400-120229400	Weak transcription	Right Ventricle	heart
35	chr11:120226400-120242400	Weak transcription	Fetal Intestine Large	intestine
36	chr11:120226400-120246800	Weak transcription	Small Intestine	intestine
37	chr11:120227000-120229400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr11:120227000-120229800	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr11:120227200-120231200	Weak transcription	Ovary	ovary
40	chr11:120227400-120229600	Enhancers	HepG2	liver
41	chr11:120227800-120229600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr11:120228000-120229200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr11:120228000-120231000	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr11:120228400-120229400	Weak transcription	Right Atrium	heart
45	chr11:120228600-120229400	Weak transcription	Psoas Muscle	Psoas
46	chr11:120228600-120231800	Weak transcription	Lung	lung

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