Variant report

Variant	rs17123861
Chromosome Location	chr11:120256337-120256338
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	chr11:120256139..120258853-chr11:120261413..120263735,2	K562	blood:

Extended variants
information (count: 71 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10502235	0.81[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10750173	0.84[JPT][hapmap]
rs10790381	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10790383	0.84[JPT][hapmap]
rs10892563	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs10892565	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10892566	0.84[JPT][hapmap]
rs10892569	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10892575	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11217821	0.84[JPT][hapmap]
rs11217843	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11217857	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11217866	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11217874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11217875	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11217878	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11601535	0.82[JPT][hapmap]
rs11823264	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11824032	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11827818	0.81[ASW][hapmap];0.88[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12270397	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12785387	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12794618	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12806740	0.84[JPT][hapmap]
rs12807097	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1812974	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1892894	0.84[JPT][hapmap]
rs1893261	0.84[JPT][hapmap]
rs2276035	0.81[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2305008	0.84[JPT][hapmap]
rs2305010	0.84[JPT][hapmap]
rs4381380	0.92[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs4936517	0.86[ASN][1000 genomes]
rs4936518	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4938799	0.84[JPT][hapmap]
rs4938802	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4938803	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4938804	0.84[JPT][hapmap]
rs4938805	0.84[JPT][hapmap]
rs4938806	0.99[ASN][1000 genomes]
rs4938807	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4938808	0.84[JPT][hapmap]
rs56693116	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6589810	0.99[ASN][1000 genomes]
rs6589812	0.84[JPT][hapmap]
rs6589813	0.97[ASN][1000 genomes]
rs7101415	0.99[ASN][1000 genomes]
rs7107211	0.87[ASN][1000 genomes]
rs7115714	0.96[ASN][1000 genomes]
rs7121779	0.84[JPT][hapmap]
rs7129944	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7131597	0.84[JPT][hapmap]
rs723937	0.84[JPT][hapmap]
rs7924772	0.96[ASN][1000 genomes]
rs7933086	0.84[JPT][hapmap]
rs7939137	0.84[JPT][hapmap]
rs7948928	0.84[JPT][hapmap]
rs894839	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 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
5	nsv1036694	chr11:120230243-120285603	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1037573	chr11:120230243-120286918	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1047982	chr11:120238962-120276373	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1050789	chr11:120238962-120286918	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
9	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
10	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
11	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
12	nsv1050709	chr11:120246224-120276373	Weak transcription Enhancers 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
13	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
rs17123861	TMEM136	cis	parietal	SCAN
rs17123861	ARHGEF12	cis	cerebellum	SCAN
rs17123861	SIDT2	cis	parietal	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120217600-120257000	Weak transcription	HSMM	muscle
2	chr11:120224800-120260800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr11:120232000-120274800	Weak transcription	Ovary	ovary
4	chr11:120251400-120261200	Weak transcription	Brain Substantia Nigra	brain
5	chr11:120252400-120256600	Weak transcription	Stomach Mucosa	stomach
6	chr11:120253000-120256400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr11:120253200-120260800	Weak transcription	Fetal Lung	lung
8	chr11:120253800-120256400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr11:120254000-120258000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr11:120254200-120256600	Enhancers	NHEK	skin
11	chr11:120254200-120256800	Enhancers	Psoas Muscle	Psoas
12	chr11:120254200-120257800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr11:120254200-120258000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr11:120254200-120258000	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr11:120254200-120258400	Enhancers	Liver	Liver
16	chr11:120254400-120257000	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr11:120254400-120257800	Enhancers	Fetal Heart	heart
18	chr11:120254400-120257800	Enhancers	NHDF-Ad	bronchial
19	chr11:120254400-120258000	Enhancers	Osteobl	bone
20	chr11:120254600-120257800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr11:120254600-120265000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr11:120254600-120266400	Weak transcription	Gastric	stomach
23	chr11:120254600-120271000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr11:120255000-120256800	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr11:120255000-120257400	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr11:120255000-120257600	Enhancers	Colon Smooth Muscle	Colon
27	chr11:120255200-120257000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr11:120255200-120257400	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr11:120255200-120258000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr11:120255400-120256400	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr11:120255400-120256400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr11:120255400-120256400	Enhancers	K562	blood
33	chr11:120255400-120256600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr11:120255400-120257200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr11:120255400-120257400	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr11:120255400-120257600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr11:120255400-120262200	Weak transcription	Right Ventricle	heart
38	chr11:120255600-120256400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr11:120255600-120256600	Weak transcription	NHLF	lung
40	chr11:120255600-120257000	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr11:120255600-120257600	Active TSS	Fetal Brain Male	brain
42	chr11:120255600-120259000	Active TSS	Fetal Brain Female	brain
43	chr11:120255600-120260800	Weak transcription	HMEC	breast
44	chr11:120255800-120256400	Active TSS	Brain Anterior Caudate	brain
45	chr11:120255800-120257000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr11:120255800-120258000	Enhancers	Adipose Nuclei	Adipose
47	chr11:120255800-120259400	Enhancers	A549	lung
48	chr11:120255800-120262000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr11:120256000-120256800	Enhancers	HUES6 Cell Line	embryonic stem cell
50	chr11:120256000-120256800	Enhancers	Small Intestine	intestine

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