Variant report

Variant	rs10892575
Chromosome Location	chr11:120291137-120291138
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10502235	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];0.85[EUR][1000 genomes]
rs10750173	0.90[JPT][hapmap]
rs10790381	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10790383	0.90[JPT][hapmap]
rs10892563	0.82[CHB][hapmap];0.80[CHD][hapmap];0.94[JPT][hapmap]
rs10892565	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10892566	0.90[JPT][hapmap]
rs10892569	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11217821	0.90[JPT][hapmap]
rs11217843	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11217857	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11217866	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11217874	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11217875	0.93[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11217878	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11217887	0.82[ASN][1000 genomes]
rs11601535	0.88[JPT][hapmap]
rs11823264	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11824032	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11827818	0.88[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs12270397	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12785387	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12794618	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12806740	0.90[JPT][hapmap]
rs12807097	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17123861	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1812974	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1892894	0.90[JPT][hapmap]
rs1893261	0.90[JPT][hapmap]
rs2276035	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2305008	0.90[JPT][hapmap]
rs2305010	0.90[JPT][hapmap]
rs4381380	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4936517	0.84[ASN][1000 genomes]
rs4936518	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4938799	0.90[JPT][hapmap]
rs4938802	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4938803	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4938804	0.89[JPT][hapmap]
rs4938805	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs4938806	0.97[ASN][1000 genomes]
rs4938807	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4938808	0.90[JPT][hapmap]
rs56693116	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6589810	0.97[ASN][1000 genomes]
rs6589812	0.90[JPT][hapmap]
rs6589813	0.99[ASN][1000 genomes]
rs7101415	0.97[ASN][1000 genomes]
rs7107211	0.85[ASN][1000 genomes]
rs7115714	0.98[ASN][1000 genomes]
rs7121779	0.90[JPT][hapmap]
rs7129944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7131597	0.90[JPT][hapmap]
rs723937	0.89[JPT][hapmap]
rs7924772	0.94[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:7 , 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	nsv1046430	chr11:120238962-120294026	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1043248	chr11:120238962-120299598	Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1051672	chr11:120238962-120314178	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1051783	chr11:120246224-120314178	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10892575	ARHGEF12	cis	cerebellum	SCAN
rs10892575	TMEM136	cis	parietal	SCAN
rs10892575	SIDT2	cis	parietal	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120265800-120295600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:120269200-120295200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr11:120270400-120292200	Weak transcription	Fetal Stomach	stomach
4	chr11:120271600-120300200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr11:120272000-120291200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr11:120272000-120291400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr11:120272000-120302400	Weak transcription	Brain Anterior Caudate	brain
8	chr11:120272200-120291400	Weak transcription	GM12878-XiMat	blood
9	chr11:120272200-120292600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr11:120272200-120292800	Weak transcription	Fetal Kidney	kidney
11	chr11:120272200-120295200	Weak transcription	Brain Angular Gyrus	brain
12	chr11:120272200-120295200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr11:120272200-120299000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr11:120272200-120315600	Weak transcription	Brain Germinal Matrix	brain
15	chr11:120272200-120315800	Weak transcription	Brain Hippocampus Middle	brain
16	chr11:120272400-120292200	Weak transcription	Fetal Intestine Small	intestine
17	chr11:120272400-120320600	Weak transcription	Psoas Muscle	Psoas
18	chr11:120274200-120295600	Weak transcription	Pancreas	Pancrea
19	chr11:120274800-120292400	Weak transcription	HepG2	liver
20	chr11:120274800-120294800	Weak transcription	A549	lung
21	chr11:120274800-120295200	Weak transcription	Small Intestine	intestine
22	chr11:120275400-120295200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr11:120275600-120295200	Weak transcription	Ovary	ovary
24	chr11:120275600-120295400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr11:120275600-120302400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr11:120275600-120302600	Weak transcription	K562	blood
27	chr11:120275600-120322200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr11:120275800-120291400	Weak transcription	Adipose Nuclei	Adipose
29	chr11:120275800-120291400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr11:120275800-120300200	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr11:120275800-120314000	Weak transcription	Right Ventricle	heart
32	chr11:120276000-120295200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr11:120276400-120295400	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr11:120276600-120302200	Weak transcription	Fetal Heart	heart
35	chr11:120276800-120295400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr11:120277600-120319800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr11:120278200-120295600	Weak transcription	Primary B cells from peripheral blood	blood
38	chr11:120278600-120291400	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr11:120278600-120295200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr11:120278800-120292600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr11:120278800-120295600	Weak transcription	Fetal Brain Female	brain
42	chr11:120279400-120295000	Weak transcription	Fetal Brain Male	brain
43	chr11:120280400-120291400	Weak transcription	Duodenum Mucosa	Duodenum
44	chr11:120280400-120299600	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr11:120281000-120291200	Weak transcription	NHLF	lung
46	chr11:120283200-120295000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr11:120284800-120295000	Weak transcription	Colon Smooth Muscle	Colon
48	chr11:120284800-120295000	Weak transcription	Fetal Lung	lung
49	chr11:120284800-120295000	Weak transcription	HMEC	breast
50	chr11:120284800-120298800	Weak transcription	NH-A	brain

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