Variant report

Variant	rs855702
Chromosome Location	chr10:93888052-93888053
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10748577	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10786029	0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs10786031	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10786033	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10882028	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10882042	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1099379	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11186755	1.00[YRI][hapmap]
rs11186914	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11186915	0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap]
rs1137825	1.00[YRI][hapmap]
rs1229578	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1229579	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12413858	1.00[YRI][hapmap]
rs12571564	1.00[YRI][hapmap]
rs12763600	1.00[YRI][hapmap]
rs12774665	1.00[YRI][hapmap]
rs1622656	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1711849	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1971471	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2254667	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs2265195	0.86[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap]
rs2676817	1.00[YRI][hapmap]
rs2676819	1.00[YRI][hapmap]
rs2676820	1.00[YRI][hapmap]
rs2676822	1.00[YRI][hapmap]
rs2767654	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2771248	0.86[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs2792022	1.00[YRI][hapmap]
rs2797639	1.00[YRI][hapmap]
rs2798254	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3781229	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3824734	0.86[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4642988	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4933227	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4933228	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4933229	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4933705	1.00[YRI][hapmap]
rs4933706	1.00[YRI][hapmap]
rs4933720	0.88[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap]
rs6583804	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs701844	0.92[ASN][1000 genomes]
rs701846	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7078559	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7087501	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7090737	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7091853	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7908721	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7919699	0.86[ASN][1000 genomes]
rs7919840	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7920520	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs833367	1.00[YRI][hapmap]
rs833372	1.00[YRI][hapmap]
rs833384	1.00[YRI][hapmap]
rs833385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs855698	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs855699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs855703	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs855704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs855706	0.86[ASN][1000 genomes]
rs855707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs855708	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs855710	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051226	chr10:93711296-93915586	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv540745	chr10:93711296-93915586	Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv975763	chr10:93822289-94105956	Enhancers Bivalent Enhancer Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv1046258	chr10:93866969-94466106	Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs855702	TNKS2	cis	parietal	SCAN
rs855702	RNLS	cis	cerebellum	SCAN
rs855702	RNLS	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:93859200-93901400	Weak transcription	Primary B cells from cord blood	blood
2	chr10:93868000-93901800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr10:93874600-93899600	Weak transcription	Duodenum Mucosa	Duodenum
4	chr10:93884400-93890600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr10:93884800-93896400	Weak transcription	Fetal Intestine Small	intestine
6	chr10:93884800-93896800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr10:93885200-93891000	Weak transcription	Small Intestine	intestine
8	chr10:93885200-93896200	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr10:93885400-93891200	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr10:93885400-93902000	Weak transcription	NHLF	lung
11	chr10:93885400-93902200	Weak transcription	Brain Angular Gyrus	brain
12	chr10:93885400-93902200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr10:93885400-93902400	Weak transcription	Brain Substantia Nigra	brain
14	chr10:93885400-93906400	Weak transcription	Aorta	Aorta
15	chr10:93885400-93906600	Weak transcription	Spleen	Spleen
16	chr10:93885400-93908400	Weak transcription	Lung	lung
17	chr10:93885600-93897800	Weak transcription	Gastric	stomach
18	chr10:93885600-93902200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr10:93885800-93896600	Weak transcription	Fetal Stomach	stomach
20	chr10:93885800-93905600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr10:93886000-93902000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr10:93886200-93889600	Weak transcription	Right Atrium	heart
23	chr10:93886200-93896800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr10:93886200-93896800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr10:93886200-93902200	Weak transcription	Brain Anterior Caudate	brain
26	chr10:93886200-93906000	Weak transcription	Esophagus	oesophagus
27	chr10:93886200-93906400	Weak transcription	Stomach Smooth Muscle	stomach
28	chr10:93886200-93906600	Weak transcription	Right Ventricle	heart
29	chr10:93886200-93907800	Weak transcription	Psoas Muscle	Psoas
30	chr10:93886200-93910800	Weak transcription	Pancreas	Pancrea
31	chr10:93886200-93911600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr10:93886400-93888600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr10:93886400-93890800	Weak transcription	Fetal Heart	heart
34	chr10:93886400-93891200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr10:93886400-93896600	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr10:93886400-93901800	Weak transcription	Hela-S3	cervix
37	chr10:93886600-93889400	Weak transcription	HepG2	liver
38	chr10:93887200-93889800	Weak transcription	Liver	Liver
39	chr10:93887400-93902200	Weak transcription	Left Ventricle	heart
40	chr10:93887600-93893400	Weak transcription	Primary B cells from peripheral blood	blood

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