Variant report

Variant	rs11217821
Chromosome Location	chr11:120202099-120202100
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:120193025..120195977-chr11:120201525..120204056,3	K562	blood:
2	chr11:120200949..120202634-chr11:120213060..120214568,2	MCF-7	breast:
3	chr11:120195931..120198930-chr11:120199219..120202161,2	MCF-7	breast:
4	chr11:120201509..120203556-chr11:120205430..120206977,2	MCF-7	breast:
5	chr11:120201225..120203829-chr11:120204191..120207304,3	K562	blood:

Variant related genes	Relation type
ENSG00000181264	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10502235	0.90[JPT][hapmap]
rs10750172	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10750173	0.88[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10790378	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10790380	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10790383	0.88[CEU][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap]
rs10892562	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10892563	0.82[ASW][hapmap];0.96[CEU][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10892564	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10892566	0.88[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10892567	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10892570	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11217840	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11217841	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11217852	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11217874	0.84[JPT][hapmap]
rs11217875	0.89[JPT][hapmap]
rs11600703	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11601535	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs11823300	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11827818	0.84[JPT][hapmap]
rs12361632	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12417581	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12420378	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12787285	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12806740	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1892894	0.88[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1893261	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]
rs2276035	0.84[JPT][hapmap]
rs2305008	0.81[ASW][hapmap];0.88[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap]
rs2305010	0.88[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap]
rs34298380	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36011588	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3809059	0.81[JPT][hapmap]
rs4381380	0.88[CEU][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.86[TSI][hapmap];0.80[YRI][hapmap]
rs4539328	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4936517	0.85[EUR][1000 genomes]
rs4938799	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.86[TSI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4938801	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4938804	0.81[ASW][hapmap];0.88[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4938805	0.84[CEU][hapmap];0.85[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs4938807	0.90[JPT][hapmap]
rs4938808	0.88[ASW][hapmap];0.88[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.86[MEX][hapmap];0.80[MKK][hapmap];0.86[TSI][hapmap];0.80[YRI][hapmap]
rs496248	0.81[JPT][hapmap]
rs61898351	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	0.81[ASW][hapmap];0.88[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7101415	0.84[EUR][1000 genomes]
rs7104639	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7107211	0.83[AMR][1000 genomes]
rs7117063	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7117321	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7118391	0.81[ASW][hapmap];0.95[GIH][hapmap];0.81[TSI][hapmap];0.81[ASN][1000 genomes]
rs7121779	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7126328	0.83[AMR][1000 genomes]
rs7126413	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7129944	0.90[JPT][hapmap]
rs7131046	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7131597	0.88[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs723937	0.88[CEU][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs7478880	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7924772	0.83[EUR][1000 genomes]
rs7924963	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7924975	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7932037	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7932658	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7933086	0.88[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7937612	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7939137	0.88[CEU][hapmap];0.85[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs7948928	0.88[CEU][hapmap];0.85[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7952529	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs894839	0.88[CEU][hapmap];0.85[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.82[MEX][hapmap];0.80[MKK][hapmap];0.83[TSI][hapmap]
rs9633919	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9633950	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][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
rs11217821	TMEM136	cis	parietal	SCAN
rs11217821	ARHGEF12	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120196400-120206400	Weak transcription	Gastric	stomach
2	chr11:120196800-120205800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:120196800-120205800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:120196800-120206200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:120197200-120205800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr11:120197200-120205800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr11:120197600-120205800	Weak transcription	Liver	Liver
8	chr11:120197800-120205600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr11:120198000-120205200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr11:120198000-120205600	Enhancers	Hela-S3	cervix
11	chr11:120198200-120205600	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr11:120198200-120205600	Weak transcription	HepG2	liver
13	chr11:120198400-120202200	Weak transcription	Fetal Intestine Small	intestine
14	chr11:120198400-120202200	Weak transcription	Stomach Mucosa	stomach
15	chr11:120198400-120204000	Weak transcription	GM12878-XiMat	blood
16	chr11:120198400-120204600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr11:120198400-120205600	Weak transcription	Duodenum Mucosa	Duodenum
18	chr11:120198400-120205800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr11:120198400-120206400	Weak transcription	Lung	lung
20	chr11:120198400-120206400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr11:120198600-120203400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:120199200-120202200	Genic enhancers	HSMM	muscle
23	chr11:120199200-120202600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr11:120199400-120202200	Weak transcription	Psoas Muscle	Psoas
25	chr11:120199400-120203200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr11:120199400-120205200	Weak transcription	Colon Smooth Muscle	Colon
27	chr11:120199600-120202200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr11:120199600-120203600	Weak transcription	K562	blood
29	chr11:120199600-120205800	Weak transcription	Right Atrium	heart
30	chr11:120199800-120202200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr11:120200200-120202400	Strong transcription	Brain Hippocampus Middle	brain
32	chr11:120200400-120202200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr11:120200400-120202400	Strong transcription	Brain Anterior Caudate	brain
34	chr11:120200400-120202600	Strong transcription	Brain Inferior Temporal Lobe	brain
35	chr11:120200400-120202800	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr11:120200400-120203000	Strong transcription	Brain Cingulate Gyrus	brain
37	chr11:120200600-120202200	Genic enhancers	Left Ventricle	heart
38	chr11:120200600-120202400	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr11:120200600-120202400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr11:120200600-120202400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr11:120200600-120202600	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr11:120200600-120202600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr11:120200600-120202600	Strong transcription	Fetal Brain Female	brain
44	chr11:120200600-120202600	Strong transcription	Fetal Muscle Trunk	muscle
45	chr11:120200600-120202800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr11:120200600-120203800	Strong transcription	Brain Germinal Matrix	brain
47	chr11:120200800-120202400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr11:120200800-120202400	Strong transcription	Brain Substantia Nigra	brain
49	chr11:120200800-120202400	Strong transcription	Fetal Kidney	kidney
50	chr11:120200800-120202800	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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