Variant report

Variant	rs12137269
Chromosome Location	chr1:113106633-113106634
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	chr1:112935217..112937989-chr1:113105345..113107131,2	K562	blood:
2	chr1:113100782..113102788-chr1:113105992..113107667,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10857961	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10857964	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10857967	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1106287	1.00[CEU][hapmap];0.83[CHB][hapmap];0.88[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap]
rs11102496	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11102498	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11102501	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11102509	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11102513	1.00[CEU][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11102514	1.00[CEU][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12029985	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12040988	0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12045227	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12049572	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12117479	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12120956	1.00[CEU][hapmap]
rs12122980	1.00[CEU][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12130243	1.00[CEU][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12140506	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12406530	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12724928	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12728311	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12756815	0.94[CEU][hapmap];0.85[YRI][hapmap]
rs17030613	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes]
rs2064711	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2273368	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.97[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2306937	0.82[AFR][1000 genomes]
rs2306940	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap]
rs2887882	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34107138	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34199214	0.83[AMR][1000 genomes]
rs34569066	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35023236	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35147679	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3737136	1.00[ASW][hapmap];0.94[CEU][hapmap];0.94[GIH][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3748656	0.89[CEU][hapmap];0.81[CHB][hapmap];0.88[GIH][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap]
rs3795819	1.00[CEU][hapmap];0.87[CHB][hapmap];0.88[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap]
rs55652172	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56135413	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60900293	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61818802	0.81[AMR][1000 genomes]
rs6679	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap]
rs9308256	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
4	nsv831081	chr1:112934920-113122640	Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv432631	chr1:113071834-113200797	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
6	esv1821231	chr1:113106020-113112746	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12137269	ST7L	cis	lymphoblastoid	seeQTL
rs12137269	SLC16A4	cis	cerebellum	SCAN
rs12137269	ST7L	Cis_1M	lymphoblastoid	RTeQTL
rs12137269	ST7L	cis	multi-tissue	Pritchard
rs12137269	DENND2C	cis	parietal	SCAN
rs12137269	GSTM1	cis	parietal	SCAN
rs12137269	WNT2B	cis	parietal	SCAN
rs12137269	AMPD1	cis	cerebellum	SCAN
rs12137269	SYT6	cis	parietal	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113058800-113119400	Weak transcription	HepG2	liver
2	chr1:113060200-113132400	Weak transcription	Pancreas	Pancrea
3	chr1:113062400-113117400	Weak transcription	Psoas Muscle	Psoas
4	chr1:113064400-113132200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:113065200-113114800	Weak transcription	Small Intestine	intestine
6	chr1:113065400-113114600	Weak transcription	Fetal Brain Male	brain
7	chr1:113066000-113114600	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr1:113066000-113132200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr1:113066200-113114400	Weak transcription	Dnd41	blood
10	chr1:113067000-113117400	Weak transcription	Fetal Thymus	thymus
11	chr1:113070400-113120600	Weak transcription	Right Ventricle	heart
12	chr1:113070600-113111600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr1:113070600-113112400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:113070600-113112400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr1:113070600-113117800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:113070600-113120200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:113070600-113132400	Weak transcription	Aorta	Aorta
18	chr1:113072000-113114400	Weak transcription	Brain Anterior Caudate	brain
19	chr1:113076400-113115200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:113080200-113117800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr1:113080800-113117400	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr1:113081200-113132200	Weak transcription	Primary B cells from cord blood	blood
23	chr1:113081400-113132400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr1:113081800-113132200	Weak transcription	Primary B cells from peripheral blood	blood
25	chr1:113082000-113116000	Weak transcription	Left Ventricle	heart
26	chr1:113082000-113117400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:113082200-113118000	Weak transcription	Lung	lung
28	chr1:113083200-113123200	Weak transcription	Right Atrium	heart
29	chr1:113083600-113111600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr1:113083600-113114400	Weak transcription	Fetal Brain Female	brain
31	chr1:113083600-113117400	Weak transcription	Brain Angular Gyrus	brain
32	chr1:113084000-113114600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr1:113084000-113131400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:113084200-113110200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:113084200-113114800	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr1:113084200-113117400	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr1:113084200-113117400	Weak transcription	Brain Germinal Matrix	brain
38	chr1:113084200-113118000	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr1:113084600-113113800	Weak transcription	Brain Hippocampus Middle	brain
40	chr1:113084600-113114400	Weak transcription	Primary T cells from cord blood	blood
41	chr1:113084600-113114600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr1:113084600-113120600	Weak transcription	Ovary	ovary
43	chr1:113084800-113137000	Weak transcription	Rectal Smooth Muscle	rectum
44	chr1:113085000-113109800	Weak transcription	Fetal Lung	lung
45	chr1:113085200-113114600	Weak transcription	Placenta	Placenta
46	chr1:113087600-113114400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr1:113087600-113125800	Weak transcription	Colon Smooth Muscle	Colon
48	chr1:113088400-113132200	Weak transcription	HMEC	breast
49	chr1:113088800-113114600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr1:113088800-113117400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links