Variant report

Variant	rs10896794
Chromosome Location	chr11:58339124-58339125
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	chr11:58308273..58310053-chr11:58338250..58340152,2	K562	blood:

Extended variants
information (count: 72 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10792172	0.88[LWK][hapmap];0.94[YRI][hapmap]
rs10896774	0.87[AMR][1000 genomes]
rs10896775	0.85[AMR][1000 genomes]
rs10896785	0.91[AMR][1000 genomes]
rs10896787	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10896788	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10896795	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10896796	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11229409	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs11229410	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs11229411	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs11229412	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs11229413	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs11229423	0.83[AMR][1000 genomes]
rs11229463	0.83[CEU][hapmap];0.84[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs11229505	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11229512	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11229519	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11229543	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11229545	0.91[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11229555	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11530830	0.89[AMR][1000 genomes]
rs11601687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11603890	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11605269	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11605297	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11605683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12269745	0.87[AMR][1000 genomes]
rs12274866	0.87[AMR][1000 genomes]
rs12279895	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs12280114	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs12283414	0.87[AMR][1000 genomes]
rs12285111	0.83[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes]
rs12286421	0.87[AMR][1000 genomes]
rs12289198	0.87[AMR][1000 genomes]
rs12290089	0.87[AMR][1000 genomes]
rs12291551	0.87[AMR][1000 genomes]
rs12294062	0.87[AMR][1000 genomes]
rs12786744	0.89[AMR][1000 genomes]
rs12787765	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12797488	0.89[AMR][1000 genomes]
rs12799215	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12800710	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12802819	0.87[AMR][1000 genomes]
rs12802960	0.87[AMR][1000 genomes]
rs12803648	0.83[AMR][1000 genomes]
rs12808544	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17474373	0.89[AMR][1000 genomes]
rs17567523	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1893902	0.83[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap]
rs1938598	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1986404	0.83[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes]
rs2275993	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2276153	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2298608	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3168135	0.91[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35279927	0.87[AMR][1000 genomes]
rs4347409	0.87[AMR][1000 genomes]
rs4506677	0.87[AMR][1000 genomes]
rs4517537	0.87[AMR][1000 genomes]
rs4519112	0.80[AMR][1000 genomes]
rs4579945	0.87[AMR][1000 genomes]
rs6591475	0.83[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes]
rs7102510	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7102852	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7110210	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7925560	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7927966	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7931394	0.87[AMR][1000 genomes]
rs8373	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[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	nsv1054205	chr11:57544264-58358509	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv528190	chr11:58336620-58347765	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Inflammatory bowel disease	23128233	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10896794	MS4A10	cis	cerebellum	SCAN
rs10896794	SERPING1	cis	parietal	SCAN
rs10896794	OR4C6	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58300000-58340600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr11:58315600-58340400	Weak transcription	Stomach Mucosa	stomach
3	chr11:58318400-58341000	Weak transcription	Right Ventricle	heart
4	chr11:58318400-58344800	Weak transcription	Fetal Brain Male	brain
5	chr11:58318600-58344400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr11:58318800-58340600	Weak transcription	NHLF	lung
7	chr11:58318800-58341400	Weak transcription	Psoas Muscle	Psoas
8	chr11:58319200-58343000	Weak transcription	Fetal Brain Female	brain
9	chr11:58320000-58341000	Weak transcription	HSMMtube	muscle
10	chr11:58320200-58340800	Weak transcription	Colon Smooth Muscle	Colon
11	chr11:58321600-58340400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr11:58321800-58340400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr11:58321800-58341200	Weak transcription	Colonic Mucosa	Colon
14	chr11:58321800-58345000	Weak transcription	Ovary	ovary
15	chr11:58322400-58344200	Weak transcription	Fetal Lung	lung
16	chr11:58329400-58341000	Weak transcription	Brain Angular Gyrus	brain
17	chr11:58329400-58342600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr11:58329400-58344400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr11:58330200-58343000	Weak transcription	Fetal Kidney	kidney
20	chr11:58330600-58345000	Weak transcription	Gastric	stomach
21	chr11:58331400-58341000	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr11:58332800-58340200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr11:58334800-58339600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
24	chr11:58335600-58340400	Weak transcription	Brain Hippocampus Middle	brain
25	chr11:58335800-58339800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr11:58335800-58340400	Weak transcription	Hela-S3	cervix
27	chr11:58336400-58340200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr11:58336800-58339200	Strong transcription	NHDF-Ad	bronchial
29	chr11:58337000-58340600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr11:58337000-58341200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr11:58337200-58343800	Weak transcription	Fetal Muscle Leg	muscle
32	chr11:58337400-58340400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr11:58337400-58340400	Weak transcription	Placenta	Placenta
34	chr11:58337400-58340800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr11:58337400-58341000	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr11:58337600-58339200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr11:58337600-58339200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr11:58337600-58340400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr11:58337600-58340400	Weak transcription	Left Ventricle	heart
40	chr11:58337600-58340400	Weak transcription	Pancreas	Pancrea
41	chr11:58337600-58340400	Weak transcription	Thymus	Thymus
42	chr11:58337600-58340800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr11:58337600-58341000	Weak transcription	Brain Anterior Caudate	brain
44	chr11:58337600-58341000	Weak transcription	Brain Substantia Nigra	brain
45	chr11:58337600-58341000	Weak transcription	Rectal Smooth Muscle	rectum
46	chr11:58337600-58341000	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr11:58337600-58341000	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr11:58337600-58341200	Weak transcription	Adipose Nuclei	Adipose
49	chr11:58337600-58342600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr11:58337600-58343000	Weak transcription	Spleen	Spleen

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