Variant report

Variant	rs10865030
Chromosome Location	chr2:99804642-99804643
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10180688	0.80[CEU][hapmap]
rs11123769	0.94[EUR][1000 genomes]
rs11123776	0.81[EUR][1000 genomes]
rs11123784	0.80[CEU][hapmap]
rs11525712	0.82[EUR][1000 genomes]
rs12993310	0.93[EUR][1000 genomes]
rs13028722	0.80[CEU][hapmap]
rs13401163	0.80[CEU][hapmap]
rs13404012	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1487271	0.93[EUR][1000 genomes]
rs1487272	0.83[EUR][1000 genomes]
rs1565054	0.90[EUR][1000 genomes]
rs1843807	0.93[EUR][1000 genomes]
rs1882598	0.80[CEU][hapmap]
rs1922625	0.80[CEU][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs1922627	0.82[EUR][1000 genomes]
rs1948101	0.82[EUR][1000 genomes]
rs2091798	0.86[EUR][1000 genomes]
rs2309577	0.80[CEU][hapmap]
rs2309615	0.80[EUR][1000 genomes]
rs2309616	0.82[EUR][1000 genomes]
rs2632285	0.84[EUR][1000 genomes]
rs35996174	0.83[EUR][1000 genomes]
rs3828162	0.80[CEU][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap]
rs4522654	0.80[CEU][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs4850896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851189	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851191	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs4851194	0.93[EUR][1000 genomes]
rs4851199	0.80[CEU][hapmap];0.80[EUR][1000 genomes]
rs6542871	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6542877	0.80[EUR][1000 genomes]
rs6712137	0.80[CEU][hapmap]
rs6728723	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6747601	0.81[EUR][1000 genomes]
rs6749029	0.80[CEU][hapmap];0.80[EUR][1000 genomes]
rs7567230	0.80[EUR][1000 genomes]
rs7567462	0.82[EUR][1000 genomes]
rs7569805	0.80[CEU][hapmap]
rs7579143	0.85[MEX][hapmap];0.91[TSI][hapmap]
rs7579999	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs7581337	0.80[EUR][1000 genomes]
rs7584705	0.80[EUR][1000 genomes]
rs7586635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs7599384	0.80[CEU][hapmap]
rs7599843	0.82[EUR][1000 genomes]
rs7602401	0.93[EUR][1000 genomes]
rs7602637	0.80[EUR][1000 genomes]
rs7603388	0.80[CEU][hapmap];0.80[EUR][1000 genomes]
rs7606279	0.80[CEU][hapmap];0.80[EUR][1000 genomes]
rs896884	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.89[MKK][hapmap];0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1013507	chr2:99729047-99861692	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv961842	chr2:99781138-99886836	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10865030	TSGA10	cis	cerebellum	SCAN
rs10865030	LIPT1	cis	multi-tissue	Pritchard
rs10865030	ARID5A	cis	parietal	SCAN
rs10865030	LIPT1	cis	parietal	SCAN
rs10865030	TSGA10	cis	multi-tissue	Pritchard
rs10865030	LYG1	cis	parietal	SCAN
rs10865030	LIPT1	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99798400-99807200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr2:99798400-99812000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:99798600-99805400	Weak transcription	Psoas Muscle	Psoas
4	chr2:99798600-99805600	Weak transcription	Brain Anterior Caudate	brain
5	chr2:99798600-99808000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr2:99798600-99808200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:99798600-99812000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:99798600-99812000	Weak transcription	Aorta	Aorta
9	chr2:99798600-99814000	Weak transcription	Right Ventricle	heart
10	chr2:99798600-99814800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr2:99798600-99815200	Weak transcription	Esophagus	oesophagus
12	chr2:99798600-99822000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr2:99798600-99836400	Weak transcription	Small Intestine	intestine
14	chr2:99798800-99804800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr2:99798800-99805200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:99798800-99805400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr2:99798800-99805600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr2:99798800-99805600	Weak transcription	Brain Substantia Nigra	brain
19	chr2:99798800-99805600	Weak transcription	Colonic Mucosa	Colon
20	chr2:99798800-99805600	Weak transcription	Fetal Intestine Large	intestine
21	chr2:99798800-99805600	Weak transcription	NH-A	brain
22	chr2:99798800-99806400	Weak transcription	Thymus	Thymus
23	chr2:99798800-99806600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr2:99798800-99807800	Weak transcription	NHDF-Ad	bronchial
25	chr2:99798800-99810800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr2:99798800-99812000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr2:99798800-99812000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:99798800-99812000	Weak transcription	Fetal Kidney	kidney
29	chr2:99798800-99815400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr2:99798800-99825600	Weak transcription	Fetal Heart	heart
31	chr2:99799000-99805400	Weak transcription	HSMM	muscle
32	chr2:99799200-99806600	Weak transcription	Brain Germinal Matrix	brain
33	chr2:99799200-99811800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr2:99799200-99813000	Weak transcription	HUVEC	blood vessel
35	chr2:99799200-99824200	Weak transcription	Fetal Brain Male	brain
36	chr2:99799400-99805400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr2:99799600-99805200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr2:99799600-99805600	Weak transcription	Colon Smooth Muscle	Colon
39	chr2:99799600-99805600	Weak transcription	Fetal Brain Female	brain
40	chr2:99799600-99807200	Weak transcription	Ovary	ovary
41	chr2:99799600-99811200	Weak transcription	HMEC	breast
42	chr2:99799600-99812600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr2:99799600-99814200	Weak transcription	NHLF	lung
44	chr2:99799800-99805600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr2:99799800-99805600	Weak transcription	Brain Hippocampus Middle	brain
46	chr2:99799800-99806200	Weak transcription	GM12878-XiMat	blood
47	chr2:99799800-99807800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr2:99799800-99811000	Weak transcription	Osteobl	bone
49	chr2:99799800-99812000	Weak transcription	Gastric	stomach
50	chr2:99799800-99814400	Weak transcription	Brain Angular Gyrus	brain

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