Variant report

Variant	rs11712653
Chromosome Location	chr3:53070875-53070876
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53069872..53071542-chr3:53073094..53075949,2	K562	blood:

Extended variants
information (count: 107 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10510761	1.00[CEU][hapmap];0.85[LWK][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11706035	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11707575	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11707780	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];1.00[EUR][1000 genomes]
rs11710292	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11710394	1.00[CEU][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11710707	0.89[EUR][1000 genomes]
rs11711773	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11713171	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713206	0.89[EUR][1000 genomes]
rs11713290	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11713859	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11713926	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs11714037	0.89[EUR][1000 genomes]
rs11714876	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes]
rs11714902	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11715231	0.84[EUR][1000 genomes]
rs11717132	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11717619	1.00[CEU][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11717715	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11718388	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718538	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11718752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11718834	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11720191	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13058817	0.93[EUR][1000 genomes]
rs13069006	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs13072395	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs13072457	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13072818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13074524	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13076033	0.91[CEU][hapmap]
rs13078834	0.89[EUR][1000 genomes]
rs13078971	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13084937	0.94[EUR][1000 genomes]
rs13085514	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13085544	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13088281	0.89[CHB][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap]
rs13091844	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13092352	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13320044	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1346719	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];1.00[EUR][1000 genomes]
rs1560333	1.00[JPT][hapmap]
rs17052726	1.00[YRI][hapmap]
rs17052727	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2336540	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2336541	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2564926	0.93[EUR][1000 genomes]
rs2564941	0.80[EUR][1000 genomes]
rs2581807	0.93[EUR][1000 genomes]
rs3097417	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34121720	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34238610	0.95[EUR][1000 genomes]
rs34244302	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34313969	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34340609	1.00[EUR][1000 genomes]
rs34493168	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34754279	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34872575	0.89[EUR][1000 genomes]
rs34933390	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34943350	0.89[EUR][1000 genomes]
rs34979715	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35076015	0.95[EUR][1000 genomes]
rs35163227	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35174175	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35230793	0.84[EUR][1000 genomes]
rs35378159	0.89[EUR][1000 genomes]
rs35384050	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35385050	0.89[EUR][1000 genomes]
rs35507120	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35720014	0.89[EUR][1000 genomes]
rs35737577	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35849389	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36090694	0.89[EUR][1000 genomes]
rs3796352	1.00[CEU][hapmap];0.83[GIH][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs3806692	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs3821872	0.96[EUR][1000 genomes]
rs4478072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58515094	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58660500	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59583591	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60887045	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60942590	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61172708	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6445555	0.91[EUR][1000 genomes]
rs6445556	0.98[EUR][1000 genomes]
rs6445557	0.98[EUR][1000 genomes]
rs71299622	0.84[EUR][1000 genomes]
rs71299700	0.81[EUR][1000 genomes]
rs71301804	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71301808	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71301809	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71301811	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71301814	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71617204	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs750474	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.98[EUR][1000 genomes]
rs7622420	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7625448	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7640293	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7645611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9756317	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.93[EUR][1000 genomes]
rs9875573	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1818974	chr3:52966316-53096394	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv876800	chr3:53038786-53113762	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv1823728	chr3:53046712-53080351	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv1820544	chr3:53046712-53096394	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv822094	chr3:53059674-53096460	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11712653	TMEM110	cis	multi-tissue	Pritchard
rs11712653	ITIH4	cis	multi-tissue	Pritchard

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53033000-53078400	Weak transcription	Aorta	Aorta
2	chr3:53048800-53077800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr3:53056600-53077800	Weak transcription	Fetal Stomach	stomach
4	chr3:53061800-53074400	Weak transcription	Osteobl	bone
5	chr3:53062200-53074400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr3:53062200-53076800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:53062200-53077000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:53062400-53071000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:53064000-53078400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:53065400-53073000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:53065400-53073000	Weak transcription	Esophagus	oesophagus
12	chr3:53065400-53074400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr3:53065400-53077600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr3:53065400-53078600	Weak transcription	Gastric	stomach
15	chr3:53065600-53072600	Weak transcription	NHEK	skin
16	chr3:53065600-53077000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:53065800-53073000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:53065800-53076200	Weak transcription	Primary B cells from cord blood	blood
19	chr3:53066200-53076800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:53068000-53077600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr3:53068200-53072000	Enhancers	Primary T cells fromperipheralblood	blood
22	chr3:53068600-53071000	Enhancers	Fetal Intestine Small	intestine
23	chr3:53068600-53071200	Enhancers	Fetal Intestine Large	intestine
24	chr3:53068600-53075000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr3:53068800-53071200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr3:53068800-53071600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr3:53068800-53071600	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr3:53068800-53071600	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr3:53068800-53071600	Enhancers	HepG2	liver
30	chr3:53068800-53077400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr3:53069000-53071000	Enhancers	A549	lung
32	chr3:53069000-53071400	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr3:53069200-53077800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr3:53069200-53077800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr3:53069800-53071000	Enhancers	Small Intestine	intestine
36	chr3:53069800-53073000	Weak transcription	Pancreas	Pancrea
37	chr3:53069800-53077600	Weak transcription	Stomach Mucosa	stomach
38	chr3:53070000-53071400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr3:53070000-53071400	Enhancers	Dnd41	blood
40	chr3:53070200-53071000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr3:53070200-53072400	Weak transcription	Liver	Liver
42	chr3:53070200-53077800	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr3:53070400-53071000	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr3:53070400-53071000	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr3:53070400-53071400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr3:53070400-53071400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr3:53070600-53071000	Enhancers	Right Ventricle	heart
48	chr3:53070600-53071200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr3:53070600-53071200	Enhancers	Fetal Heart	heart
50	chr3:53070600-53071200	Enhancers	Sigmoid Colon	Sigmoid Colon

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