Variant report

Variant	rs12486371
Chromosome Location	chr3:105518948-105518949
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1042852	0.91[ASW][hapmap]
rs11919893	0.83[CEU][hapmap]
rs12485832	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12487841	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12496588	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12497428	0.83[CEU][hapmap]
rs12632980	0.83[CEU][hapmap]
rs13090949	0.83[CEU][hapmap]
rs13317635	0.91[ASW][hapmap]
rs13433776	0.83[CEU][hapmap]
rs1443108	1.00[ASW][hapmap]
rs1867189	1.00[ASW][hapmap]
rs2301043	1.00[ASW][hapmap]
rs2305035	1.00[ASW][hapmap]
rs2305036	1.00[ASW][hapmap]
rs2455887	0.86[ASN][1000 genomes]
rs3772512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772515	1.00[ASW][hapmap]
rs56344829	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58882222	0.86[ASN][1000 genomes]
rs6437616	0.88[CEU][hapmap]
rs6437623	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6780432	0.83[CEU][hapmap]
rs6791765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793018	1.00[ASN][1000 genomes]
rs6796362	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72997629	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72997684	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7619647	1.00[ASW][hapmap]
rs7624530	0.91[ASW][hapmap]
rs7634195	0.83[CEU][hapmap]
rs7638504	0.83[CEU][hapmap]
rs7639888	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7641825	0.84[ASW][hapmap]
rs7650147	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894541	0.83[CEU][hapmap]
rs9657910	1.00[CHB][hapmap];1.00[TSI][hapmap]
rs9811776	0.83[CEU][hapmap]
rs9814582	0.83[CEU][hapmap]
rs9820060	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838755	0.83[CEU][hapmap]
rs9841798	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9872895	0.81[CEU][hapmap]
rs9876110	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9880744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9880861	1.00[ASW][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	nsv877309	chr3:105373836-105542435	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	esv2755185	chr3:105378310-105597310	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105483200-105555200	Weak transcription	Placenta	Placenta
2	chr3:105486800-105519000	Weak transcription	Esophagus	oesophagus
3	chr3:105489600-105525400	Weak transcription	Fetal Intestine Small	intestine
4	chr3:105505000-105527800	Weak transcription	Pancreas	Pancrea
5	chr3:105505000-105548200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:105509800-105527800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr3:105510600-105521200	Weak transcription	Fetal Brain Male	brain
8	chr3:105511400-105566400	Weak transcription	Aorta	Aorta
9	chr3:105511800-105520400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr3:105512000-105520600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:105512200-105519000	Weak transcription	Psoas Muscle	Psoas
12	chr3:105512200-105519000	Weak transcription	Right Atrium	heart
13	chr3:105512200-105519200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr3:105512200-105520200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:105512200-105520400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:105512200-105527200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr3:105512200-105534200	Weak transcription	Left Ventricle	heart
18	chr3:105512400-105524400	Weak transcription	NHLF	lung
19	chr3:105512600-105520400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr3:105512600-105524000	Weak transcription	HSMMtube	muscle
21	chr3:105512600-105524600	Weak transcription	Colon Smooth Muscle	Colon
22	chr3:105512600-105525200	Weak transcription	HSMM	muscle
23	chr3:105514400-105521600	Enhancers	Primary B cells from peripheral blood	blood
24	chr3:105515400-105528200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:105515400-105539000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr3:105515800-105521600	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr3:105516000-105519400	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr3:105516000-105521600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr3:105516000-105521600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr3:105516200-105522200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr3:105516400-105519400	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr3:105516400-105521000	Enhancers	Primary T cells from cord blood	blood
33	chr3:105516400-105521800	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr3:105516600-105519400	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr3:105516600-105519400	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr3:105516600-105519800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr3:105516600-105522000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr3:105516600-105523000	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr3:105516800-105519800	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr3:105517200-105519400	Enhancers	Muscle Satellite Cultured Cells	--
41	chr3:105517400-105519600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:105517400-105519800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr3:105517800-105519000	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr3:105517800-105519000	Weak transcription	Ovary	ovary
45	chr3:105517800-105519000	Weak transcription	Small Intestine	intestine
46	chr3:105517800-105519200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr3:105517800-105519200	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr3:105517800-105519600	Genic enhancers	Osteobl	bone
49	chr3:105517800-105519800	Weak transcription	Fetal Heart	heart
50	chr3:105517800-105520400	Weak transcription	Brain Hippocampus Middle	brain

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