Variant report

Variant	rs10513016
Chromosome Location	chr3:136343945-136343946
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:136340612..136342191-chr3:136342513..136345195,2	MCF-7	breast:
2	chr3:136342393..136347212-chr3:136468546..136473681,8	MCF-7	breast:
3	chr3:136343802..136345688-chr3:136349798..136351830,2	MCF-7	breast:
4	chr3:136341644..136343243-chr3:136343703..136345406,2	K562	blood:

Variant related genes	Relation type
ENSG00000118007	Chromatin interaction
ENSG00000261758	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs16843991	1.00[CHB][hapmap]
rs16844056	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17365351	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17466223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35375192	1.00[CHB][hapmap]
rs35644083	1.00[CHB][hapmap]
rs3931416	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs4336059	1.00[CHB][hapmap]
rs55763637	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56218376	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs56308712	0.81[EUR][1000 genomes]
rs56888009	0.96[EUR][1000 genomes]
rs57466072	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57681357	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58636237	0.85[EUR][1000 genomes]
rs59361983	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59616231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59696368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60014495	0.94[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs60270684	0.82[AFR][1000 genomes]
rs6439642	1.00[CHB][hapmap]
rs66470158	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66471262	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66637228	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66739346	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66902780	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs66973954	0.94[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs67231188	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67236827	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67281610	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67303976	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs67305360	0.94[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs67546863	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs67621498	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6765239	1.00[CHB][hapmap]
rs67663578	0.94[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6773495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6773604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap]
rs67794070	0.94[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs67888773	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67902591	0.85[EUR][1000 genomes]
rs67923745	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6800969	1.00[CHB][hapmap]
rs68018658	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6804194	1.00[CHB][hapmap]
rs72975363	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73226130	0.81[EUR][1000 genomes]
rs73228025	0.91[EUR][1000 genomes]
rs73228037	0.94[EUR][1000 genomes]
rs73228040	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73230052	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73230077	0.85[EUR][1000 genomes]
rs73230078	0.85[EUR][1000 genomes]
rs73230095	0.83[EUR][1000 genomes]
rs73231917	0.81[EUR][1000 genomes]
rs7623824	1.00[CHB][hapmap]
rs7636806	0.94[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7644471	1.00[CHB][hapmap]
rs7646563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7646723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs923001	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9820513	1.00[CHB][hapmap]
rs9869957	1.00[CHB][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	nsv948461	chr3:135969755-136349636	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv460861	chr3:136222954-136425600	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv591851	chr3:136222954-136425600	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10513016	STAG1	cis	cerebellum	SCAN
rs10513016	TMEM22	cis	cerebellum	SCAN
rs10513016	IL20RB	cis	Nerve Tibial	GTEx
rs10513016	VCAN	trans	cerebellum	SCAN
rs10513016	ATP1B3	cis	cerebellum	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136248200-136349200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr3:136268200-136351200	Weak transcription	Esophagus	oesophagus
3	chr3:136290000-136351600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:136297200-136345400	Weak transcription	Colon Smooth Muscle	Colon
5	chr3:136297200-136351200	Weak transcription	Pancreas	Pancrea
6	chr3:136298600-136351600	Weak transcription	HSMM	muscle
7	chr3:136300200-136351200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:136308000-136357400	Weak transcription	Lung	lung
9	chr3:136313400-136344000	Weak transcription	Fetal Heart	heart
10	chr3:136315400-136356400	Weak transcription	Brain Anterior Caudate	brain
11	chr3:136315800-136344400	Weak transcription	Small Intestine	intestine
12	chr3:136315800-136346800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr3:136315800-136355600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr3:136315800-136361000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:136316000-136364400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr3:136319000-136344000	Weak transcription	NH-A	brain
17	chr3:136320800-136356800	Weak transcription	Ovary	ovary
18	chr3:136322200-136355200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:136323200-136347000	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr3:136323400-136347200	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr3:136323400-136362000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:136323800-136347000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr3:136324200-136346600	Weak transcription	Primary B cells from cord blood	blood
24	chr3:136324200-136363600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr3:136327400-136357400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr3:136327800-136346800	Weak transcription	Primary hematopoietic stem cells	blood
27	chr3:136328000-136344600	Weak transcription	Left Ventricle	heart
28	chr3:136328000-136350200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr3:136328000-136351200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:136328200-136346800	Weak transcription	Fetal Muscle Trunk	muscle
31	chr3:136330200-136344000	Weak transcription	GM12878-XiMat	blood
32	chr3:136331800-136344000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:136331800-136349400	Weak transcription	NHDF-Ad	bronchial
34	chr3:136331800-136350000	Weak transcription	NHLF	lung
35	chr3:136332800-136344800	Weak transcription	Placenta	Placenta
36	chr3:136335000-136344200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr3:136335600-136349800	Weak transcription	Osteobl	bone
38	chr3:136335600-136350600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr3:136335600-136357400	Weak transcription	Psoas Muscle	Psoas
40	chr3:136335800-136350200	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr3:136336200-136344800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr3:136336200-136364800	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr3:136336400-136346600	Weak transcription	Adipose Nuclei	Adipose
44	chr3:136336400-136350200	Weak transcription	Gastric	stomach
45	chr3:136336400-136351400	Weak transcription	Right Ventricle	heart
46	chr3:136336600-136346400	Weak transcription	Fetal Thymus	thymus
47	chr3:136338200-136344000	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr3:136338400-136344000	Weak transcription	Fetal Lung	lung
49	chr3:136338400-136349800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr3:136338600-136345800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links