Variant report

Variant	rs1893261
Chromosome Location	chr11:120198093-120198094
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	chr11:120105904..120108316-chr11:120197614..120199213,2	K562	blood:
2	chr11:120174600..120176592-chr11:120196059..120198854,2	K562	blood:

Variant related genes	Relation type
ENSG00000137709	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10502235	0.90[JPT][hapmap]
rs10750172	0.80[EUR][1000 genomes]
rs10750173	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs10790378	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10790380	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10790383	0.88[CEU][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs10892562	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10892563	0.96[CEU][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10892564	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10892566	0.88[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs10892567	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10892570	0.80[AMR][1000 genomes]
rs11217821	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11217840	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11217841	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11217852	0.81[AMR][1000 genomes]
rs11217874	0.84[JPT][hapmap]
rs11217875	0.89[JPT][hapmap]
rs11600703	0.81[AMR][1000 genomes]
rs11601535	1.00[JPT][hapmap]
rs11823300	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11827818	0.84[JPT][hapmap]
rs12361632	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12417581	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12787285	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12806740	1.00[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1892894	0.88[CEU][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2276035	0.84[JPT][hapmap]
rs2305008	0.88[CEU][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs2305010	0.88[CEU][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs34298380	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36011588	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3809059	0.81[JPT][hapmap]
rs4381380	0.88[CEU][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap]
rs4539328	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4936517	0.85[EUR][1000 genomes]
rs4938799	0.96[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4938801	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4938804	0.88[CEU][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs4938805	0.84[CEU][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs4938807	0.90[JPT][hapmap]
rs4938808	0.88[CEU][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs496248	0.81[JPT][hapmap]
rs61898351	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs632137	0.81[JPT][hapmap]
rs6589810	0.84[EUR][1000 genomes]
rs6589811	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6589812	0.88[CEU][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap]
rs7101415	0.84[EUR][1000 genomes]
rs7104639	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7107211	0.83[AMR][1000 genomes]
rs7117063	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7117321	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7118391	0.98[GIH][hapmap];0.81[TSI][hapmap]
rs7121779	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7126328	0.83[AMR][1000 genomes]
rs7126413	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7129944	0.90[JPT][hapmap]
rs7131046	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7131597	0.88[CEU][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs723937	0.88[CEU][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs7478880	0.82[AMR][1000 genomes]
rs7924772	0.83[EUR][1000 genomes]
rs7924963	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7924975	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7932037	0.80[AMR][1000 genomes]
rs7932658	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7933086	0.88[CEU][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes]
rs7939137	0.88[CEU][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs7948928	0.88[CEU][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes]
rs7952529	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs894839	0.88[CEU][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap]
rs9633919	0.81[AMR][1000 genomes]
rs9633950	0.80[AMR][1000 genomes];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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1893261	TMEM136	cis	parietal	SCAN
rs1893261	ARHGEF12	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120195800-120198200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr11:120196400-120206400	Weak transcription	Gastric	stomach
3	chr11:120196600-120198200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
4	chr11:120196600-120198400	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr11:120196600-120200600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr11:120196600-120200800	Weak transcription	Esophagus	oesophagus
7	chr11:120196800-120198200	Enhancers	Fetal Lung	lung
8	chr11:120196800-120198400	Flanking Active TSS	Brain Hippocampus Middle	brain
9	chr11:120196800-120198400	Enhancers	Sigmoid Colon	Sigmoid Colon
10	chr11:120196800-120198800	Enhancers	Fetal Intestine Large	intestine
11	chr11:120196800-120200600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr11:120196800-120205800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:120196800-120205800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr11:120196800-120206200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr11:120197000-120198200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr11:120197000-120198200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr11:120197000-120198400	Enhancers	Brain Germinal Matrix	brain
18	chr11:120197000-120198400	Enhancers	Fetal Brain Male	brain
19	chr11:120197000-120198400	Enhancers	Fetal Intestine Small	intestine
20	chr11:120197000-120198400	Enhancers	Stomach Mucosa	stomach
21	chr11:120197000-120198400	Enhancers	HSMM	muscle
22	chr11:120197000-120199200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr11:120197000-120199200	Weak transcription	Spleen	Spleen
24	chr11:120197000-120199400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr11:120197000-120200600	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr11:120197000-120200800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr11:120197000-120201800	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr11:120197200-120198200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr11:120197200-120198200	Enhancers	HepG2	liver
30	chr11:120197200-120198400	Enhancers	Primary hematopoietic stem cells	blood
31	chr11:120197200-120198400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr11:120197200-120198400	Flanking Active TSS	A549	lung
33	chr11:120197200-120198600	Enhancers	Brain Substantia Nigra	brain
34	chr11:120197200-120199200	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr11:120197200-120199200	Weak transcription	Fetal Kidney	kidney
36	chr11:120197200-120199400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr11:120197200-120199600	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr11:120197200-120200600	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr11:120197200-120200600	Weak transcription	Adipose Nuclei	Adipose
40	chr11:120197200-120200600	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr11:120197200-120200600	Weak transcription	Fetal Stomach	stomach
42	chr11:120197200-120200600	Weak transcription	Left Ventricle	heart
43	chr11:120197200-120200800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr11:120197200-120201000	Weak transcription	HMEC	breast
45	chr11:120197200-120205800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr11:120197200-120205800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr11:120197400-120198200	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr11:120197400-120198200	Flanking Active TSS	NHLF	lung
49	chr11:120197400-120198400	Enhancers	Brain Angular Gyrus	brain
50	chr11:120197400-120198400	Enhancers	Fetal Brain Female	brain

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