Variant report

Variant	rs10898894
Chromosome Location	chr11:72700779-72700780
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10437750	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10793048	0.86[YRI][hapmap]
rs10793049	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[ASN][1000 genomes]
rs10793054	0.95[YRI][hapmap]
rs10793055	0.85[ASW][hapmap];0.97[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs10793056	0.93[ASW][hapmap];0.92[CEU][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10898881	0.82[YRI][hapmap]
rs10898885	0.86[YRI][hapmap]
rs10898895	0.91[CHB][hapmap];0.95[YRI][hapmap]
rs10898896	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10898900	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11235612	0.91[CHB][hapmap];0.86[CHD][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap]
rs11235651	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12288580	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12289752	0.83[ASN][1000 genomes]
rs12293726	0.84[ASN][1000 genomes]
rs12294533	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1982585	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2187494	0.82[YRI][hapmap]
rs2276379	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[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];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2282613	0.82[CHD][hapmap]
rs2303969	0.91[CHB][hapmap];1.00[YRI][hapmap]
rs4394861	0.86[YRI][hapmap]
rs4944816	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55671951	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60355221	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6592500	0.86[YRI][hapmap]
rs6592508	0.93[ASW][hapmap];0.92[CEU][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7104158	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7925928	0.95[YRI][hapmap]
rs7936751	0.95[YRI][hapmap]
rs7937701	0.92[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs7943424	0.80[ASW][hapmap];0.86[GIH][hapmap];0.91[YRI][hapmap]
rs9645708	0.86[CHB][hapmap];0.86[CHD][hapmap];0.97[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][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	esv2422418	chr11:72646518-72807865	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv555411	chr11:72647296-72800970	Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10898894	ARAP1	cis	cerebellum	SCAN
rs10898894	KRTAP5-11	cis	cerebellum	SCAN
rs10898894	NEU3	cis	parietal	SCAN
rs10898894	ATG16L2	cis	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:72636400-72712600	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr11:72637000-72721600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:72649000-72721600	Weak transcription	Thymus	Thymus
4	chr11:72666600-72721600	Weak transcription	Lung	lung
5	chr11:72669800-72721800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr11:72673000-72708000	Weak transcription	Colon Smooth Muscle	Colon
7	chr11:72675800-72700800	Weak transcription	Spleen	Spleen
8	chr11:72681800-72720200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr11:72682000-72701400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr11:72682000-72710600	Weak transcription	Aorta	Aorta
11	chr11:72682800-72700800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr11:72682800-72721600	Weak transcription	Right Ventricle	heart
13	chr11:72683000-72706600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr11:72684000-72701000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr11:72684000-72712800	Weak transcription	Small Intestine	intestine
16	chr11:72684000-72721600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr11:72686600-72721600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr11:72687600-72700800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr11:72687600-72705000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr11:72687600-72708600	Weak transcription	NHDF-Ad	bronchial
21	chr11:72687600-72722200	Weak transcription	NHLF	lung
22	chr11:72687600-72724200	Weak transcription	HMEC	breast
23	chr11:72688400-72706200	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr11:72688600-72721600	Weak transcription	Brain Germinal Matrix	brain
25	chr11:72689800-72700800	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr11:72689800-72701000	Strong transcription	Dnd41	blood
27	chr11:72689800-72706800	Weak transcription	Esophagus	oesophagus
28	chr11:72689800-72717800	Weak transcription	Psoas Muscle	Psoas
29	chr11:72689800-72718400	Weak transcription	Fetal Intestine Small	intestine
30	chr11:72690800-72702000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr11:72692600-72701000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr11:72693200-72701400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr11:72693400-72721600	Weak transcription	Left Ventricle	heart
34	chr11:72693600-72708200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr11:72694400-72708000	Weak transcription	Rectal Smooth Muscle	rectum
36	chr11:72695000-72700800	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr11:72695400-72705200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr11:72695600-72720400	Weak transcription	Adipose Nuclei	Adipose
39	chr11:72695800-72720000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr11:72696000-72705200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr11:72696000-72715400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr11:72696000-72720200	Weak transcription	Fetal Intestine Large	intestine
43	chr11:72696000-72720800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr11:72696000-72724000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr11:72696600-72708000	Weak transcription	Duodenum Mucosa	Duodenum
46	chr11:72696800-72702000	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr11:72697000-72718400	Weak transcription	Fetal Muscle Leg	muscle
48	chr11:72697000-72721600	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr11:72697200-72700800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr11:72697200-72705000	Weak transcription	Fetal Thymus	thymus

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