Variant report

Variant	rs12231693
Chromosome Location	chr12:60130423-60130424
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:60113980..60116792-chr12:60129160..60132180,3	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10431557	1.00[ASW][hapmap];0.91[CHB][hapmap];0.85[GIH][hapmap];0.81[LWK][hapmap];0.84[MEX][hapmap];0.85[MKK][hapmap];0.88[YRI][hapmap]
rs10506398	0.89[ASW][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.85[LWK][hapmap];0.84[MEX][hapmap];0.85[MKK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10506399	0.95[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877338	0.95[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs10877342	0.83[CHD][hapmap]
rs11173124	0.89[ASN][1000 genomes]
rs11173126	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11173133	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11173134	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11173137	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11173158	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11173159	0.90[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12227214	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12227244	0.86[CEU][hapmap];0.90[CHB][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs12227270	0.81[ASW][hapmap];0.91[CHB][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs12231311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12231740	0.89[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[GIH][hapmap];0.85[LWK][hapmap];0.92[MEX][hapmap];0.80[MKK][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12232002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12812799	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12816935	0.95[CEU][hapmap];0.94[CHB][hapmap];0.82[EUR][1000 genomes]
rs17572877	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17572912	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17649424	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17650311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1795884	0.91[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs1795896	0.95[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs2365317	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2365318	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2706295	0.89[ASN][1000 genomes]
rs2706306	0.95[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs2706309	0.95[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs2706319	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2711655	0.95[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs2711656	0.95[CHB][hapmap];0.87[CHD][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs2711659	0.90[CHB][hapmap];0.88[CHD][hapmap];0.89[ASN][1000 genomes]
rs2711668	0.95[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs2711670	0.90[ASN][1000 genomes]
rs2711672	0.90[ASN][1000 genomes]
rs2711677	0.90[ASN][1000 genomes]
rs2711691	0.89[ASN][1000 genomes]
rs34264510	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34639075	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34785387	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35218918	0.84[ASN][1000 genomes]
rs35365387	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35518979	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35971116	0.83[ASN][1000 genomes]
rs3763980	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4583011	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56682442	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61174819	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6581274	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66802005	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66861118	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs68028492	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7133415	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7136019	0.83[EUR][1000 genomes]
rs7303876	1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7979504	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9705733	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9788077	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs995342	1.00[ASW][hapmap];0.85[CEU][hapmap];0.83[MKK][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	nsv869425	chr12:59746898-60479741	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	esv3365928	chr12:60042531-60343212	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv899132	chr12:60087572-60211476	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12231693	SLC16A7	cis	multi-tissue	Pritchard
rs12231693	SLC16A7	cis	lymphoblastoid	seeQTL
rs12231693	KIF5A	cis	cerebellum	SCAN
rs12231693	SLC16A7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:60069600-60131400	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr12:60099600-60143200	Weak transcription	Primary B cells from peripheral blood	blood
3	chr12:60100000-60175200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr12:60104200-60138000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:60110200-60141400	Weak transcription	Dnd41	blood
6	chr12:60113000-60143600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr12:60124000-60168800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr12:60126000-60130800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:60126200-60138600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr12:60126400-60130600	Weak transcription	Brain Hippocampus Middle	brain
11	chr12:60127000-60130600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr12:60127200-60131400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr12:60127800-60143000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr12:60127800-60143200	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr12:60128000-60139000	Weak transcription	Fetal Stomach	stomach
16	chr12:60128200-60133800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr12:60128200-60143000	Weak transcription	Gastric	stomach
18	chr12:60128400-60130600	Weak transcription	Aorta	Aorta
19	chr12:60128400-60138000	Weak transcription	Esophagus	oesophagus
20	chr12:60128400-60138200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr12:60128400-60139000	Weak transcription	Fetal Thymus	thymus
22	chr12:60128400-60140000	Weak transcription	Thymus	Thymus
23	chr12:60128600-60130600	Weak transcription	Right Ventricle	heart
24	chr12:60129800-60131000	Strong transcription	Primary B cells from cord blood	blood
25	chr12:60129800-60131400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:60129800-60131600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr12:60129800-60131600	Enhancers	Hela-S3	cervix
28	chr12:60129800-60131600	Enhancers	NHLF	lung
29	chr12:60129800-60131600	Enhancers	Osteobl	bone
30	chr12:60129800-60132400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr12:60130000-60131600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:60130200-60130600	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr12:60130200-60130600	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr12:60130200-60130800	Enhancers	Spleen	Spleen
35	chr12:60130200-60130800	Enhancers	NH-A	brain
36	chr12:60130200-60131000	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr12:60130200-60131000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr12:60130200-60131000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:60130200-60131000	Strong transcription	Primary T cells from cord blood	blood
40	chr12:60130200-60131000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr12:60130200-60131000	Enhancers	Muscle Satellite Cultured Cells	--
42	chr12:60130200-60131000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr12:60130200-60131000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr12:60130200-60131000	Enhancers	Fetal Heart	heart
45	chr12:60130200-60131000	Genic enhancers	Left Ventricle	heart
46	chr12:60130200-60131000	Enhancers	Pancreas	Pancrea
47	chr12:60130200-60131000	Enhancers	Right Atrium	heart
48	chr12:60130200-60131000	Flanking Active TSS	NHDF-Ad	bronchial
49	chr12:60130200-60131200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr12:60130200-60131200	Enhancers	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links