Variant report

Variant	rs12087284
Chromosome Location	chr1:172511969-172511970
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:172509695..172512146-chr1:172529892..172531866,2	K562	blood:
2	chr1:172511128..172513343-chr1:172514678..172516974,2	K562	blood:
3	chr1:172510611..172514641-chr1:172517107..172521407,5	K562	blood:
4	chr1:172411247..172413190-chr1:172511240..172513810,2	MCF-7	breast:
5	chr1:172511443..172515146-chr1:172549683..172552996,3	K562	blood:
6	chr1:172509473..172512440-chr1:172512519..172514495,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135845	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10157500	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10157519	0.85[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs10218613	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10489280	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10752994	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.91[ASN][1000 genomes]
rs10798040	0.86[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10911856	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10912058	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10912080	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10912083	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10912084	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11805370	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12121051	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12146100	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1894625	1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1894626	0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs2097492	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2097493	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2097494	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2097498	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2157420	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2227188	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2285144	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2422144	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2472550	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2472552	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2639621	0.81[EUR][1000 genomes]
rs3752515	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3768444	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4145436	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4433434	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5014539	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6424973	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6425007	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6656713	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6686080	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6686157	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6695152	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7525372	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7531652	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs7539231	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7539443	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs763108	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9425646	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872547	chr1:172511969-172545832	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12087284	SUCO	cis	Muscle Skeletal	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172503400-172528600	Weak transcription	Aorta	Aorta
2	chr1:172503400-172528600	Weak transcription	Lung	lung
3	chr1:172503600-172513600	Weak transcription	Psoas Muscle	Psoas
4	chr1:172503600-172520200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr1:172503600-172531600	Weak transcription	Esophagus	oesophagus
6	chr1:172503800-172529000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr1:172503800-172534200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr1:172504000-172524400	Weak transcription	HSMM	muscle
9	chr1:172504200-172515200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:172504200-172527000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr1:172504400-172519400	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr1:172504800-172516200	Weak transcription	HUVEC	blood vessel
13	chr1:172505200-172518800	Weak transcription	Brain Angular Gyrus	brain
14	chr1:172505800-172519600	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr1:172506000-172512000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:172506000-172519000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr1:172506000-172532600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:172506200-172525000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr1:172506200-172526200	Weak transcription	Fetal Intestine Large	intestine
20	chr1:172506200-172528400	Weak transcription	Fetal Stomach	stomach
21	chr1:172507000-172516000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:172507200-172516800	Weak transcription	Brain Germinal Matrix	brain
23	chr1:172507200-172518400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr1:172507400-172513000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:172507400-172513400	Weak transcription	K562	blood
26	chr1:172507400-172513800	Weak transcription	Stomach Mucosa	stomach
27	chr1:172507400-172515000	Weak transcription	Right Atrium	heart
28	chr1:172507400-172516400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr1:172507400-172517600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr1:172507400-172518400	Weak transcription	NHEK	skin
31	chr1:172507400-172523000	Weak transcription	NHDF-Ad	bronchial
32	chr1:172507400-172526400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr1:172507400-172528600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:172507600-172512000	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr1:172507600-172512000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:172507600-172512200	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr1:172508000-172517400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:172508200-172513000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr1:172508200-172514400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr1:172508200-172519200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:172508200-172526400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr1:172508800-172515200	Enhancers	Primary neutrophils fromperipheralblood	blood
43	chr1:172509200-172512200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr1:172509200-172515600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr1:172509400-172513200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr1:172509400-172530800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr1:172509600-172514200	Weak transcription	Thymus	Thymus
48	chr1:172510000-172512200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr1:172510000-172512800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr1:172510000-172513400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links