Variant report

Variant	rs10882028
Chromosome Location	chr10:93943900-93943901
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10748577	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs10748579	0.85[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap]
rs10786029	0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs10786031	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10786033	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10786037	0.85[CEU][hapmap]
rs10882042	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1099379	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11186914	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs11186915	0.88[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1229578	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1229579	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1622656	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs1711849	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1971471	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2254667	0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2255718	1.00[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs2265195	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs2767654	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2771248	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2771256	1.00[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs2797639	1.00[YRI][hapmap]
rs2798254	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3781229	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3824734	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[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];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4642988	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4933227	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4933228	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4933229	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4933720	0.88[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs6583804	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs701844	0.83[ASN][1000 genomes]
rs701846	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7071943	0.83[ASN][1000 genomes]
rs7078559	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7087501	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7090737	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7091853	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7897555	0.85[ASN][1000 genomes]
rs7908721	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7914436	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7919840	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7920520	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[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];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs855698	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs855699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs855702	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]
rs855703	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs855704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs855707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs855708	0.86[ASN][1000 genomes]
rs855710	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs913649	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]

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	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
2	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10882028	TNKS2	cis	parietal	SCAN
rs10882028	TPBG	trans	lymphoblastoid	seeQTL
rs10882028	RNLS	cis	cerebellum	SCAN
rs10882028	RNLS	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:93911800-93953200	Weak transcription	Pancreas	Pancrea
2	chr10:93926400-93976000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr10:93926600-93976000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr10:93926800-93982400	Weak transcription	HSMMtube	muscle
5	chr10:93927000-93947600	Weak transcription	Primary B cells from cord blood	blood
6	chr10:93927000-93963800	Weak transcription	Brain Angular Gyrus	brain
7	chr10:93927000-93966200	Weak transcription	Ovary	ovary
8	chr10:93927000-93970800	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr10:93927200-93967600	Weak transcription	Adipose Nuclei	Adipose
10	chr10:93927200-93980400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr10:93927400-93960000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr10:93927400-93966600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr10:93927400-93970800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr10:93927400-93997800	Weak transcription	Fetal Intestine Large	intestine
15	chr10:93928800-93949000	Weak transcription	Liver	Liver
16	chr10:93929200-93984800	Weak transcription	Fetal Intestine Small	intestine
17	chr10:93929400-93967800	Weak transcription	Colon Smooth Muscle	Colon
18	chr10:93930000-93958200	Weak transcription	Hela-S3	cervix
19	chr10:93934200-93949400	Weak transcription	Lung	lung
20	chr10:93934200-93976200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr10:93936600-93958000	Weak transcription	Small Intestine	intestine
22	chr10:93937200-93946600	Weak transcription	GM12878-XiMat	blood
23	chr10:93937200-93950600	Weak transcription	HepG2	liver
24	chr10:93940200-93971200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr10:93940600-93944400	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr10:93940600-93945800	Weak transcription	Left Ventricle	heart
27	chr10:93940600-93946400	Weak transcription	Psoas Muscle	Psoas
28	chr10:93940600-93958400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr10:93940600-93970800	Weak transcription	Fetal Stomach	stomach
30	chr10:93941400-93947800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr10:93941600-93944800	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr10:93941600-93947000	Weak transcription	Brain Substantia Nigra	brain
33	chr10:93941600-93948200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr10:93941600-93958000	Weak transcription	Brain Anterior Caudate	brain
35	chr10:93941600-93958000	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr10:93941800-93944800	Weak transcription	Fetal Heart	heart
37	chr10:93941800-93944800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr10:93941800-93958000	Weak transcription	Brain Hippocampus Middle	brain
39	chr10:93941800-93968000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr10:93941800-93971200	Weak transcription	Primary B cells from peripheral blood	blood
41	chr10:93942200-93953600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr10:93943400-93947600	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr10:93943600-93958200	Weak transcription	K562	blood

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