Variant report

Variant	rs12128131
Chromosome Location	chr1:93546299-93546300
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:93492630..93494568-chr1:93544878..93547230,2	K562	blood:
2	chr1:93543004..93547095-chr1:93643826..93649088,10	K562	blood:
3	chr1:93544684..93546350-chr1:93912663..93915157,2	MCF-7	breast:
4	chr1:93543004..93547588-chr1:93644888..93649088,6	K562	blood:
5	chr1:93296076..93299049-chr1:93541677..93546567,5	K562	blood:

Variant related genes	Relation type
ENSG00000137942	Chromatin interaction
ENSG00000117500	Chromatin interaction
ENSG00000122483	Chromatin interaction
ENSG00000122406	Chromatin interaction
ENSG00000251837	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1010476	0.89[CHB][hapmap]
rs1057257	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1060622	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10782955	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10874759	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10874762	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10874764	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1088318	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11164870	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11164871	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11164876	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11164879	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11164880	0.80[EUR][1000 genomes]
rs11164881	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12030549	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12030843	0.95[CHB][hapmap]
rs12038699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12044557	0.94[CHB][hapmap]
rs12044657	0.84[EUR][1000 genomes]
rs12118230	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12118262	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12124011	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12130734	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12139009	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12139633	0.81[EUR][1000 genomes]
rs12385720	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1335679	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1474927	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1535701	0.80[EUR][1000 genomes]
rs1572343	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1856027	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1932314	0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2152358	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2208044	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2255722	0.89[CHB][hapmap]
rs2281524	0.89[CHB][hapmap]
rs2281525	0.85[CHB][hapmap]
rs2295423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2295424	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2296558	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2297707	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2484486	0.89[CHB][hapmap]
rs2749732	0.84[CHB][hapmap]
rs2765545	0.95[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2783489	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs2783490	0.89[CHB][hapmap]
rs2783495	0.89[CHB][hapmap]
rs2783499	0.94[CHB][hapmap]
rs2783500	0.94[CHB][hapmap]
rs2783501	0.95[CHB][hapmap]
rs2815429	0.84[CHB][hapmap]
rs35940311	0.85[AMR][1000 genomes]
rs3754184	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3754186	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs3904665	0.81[CHB][hapmap]
rs3904666	0.89[CHB][hapmap]
rs4000699	0.81[EUR][1000 genomes]
rs4484937	0.94[CHB][hapmap]
rs4847235	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4847398	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4847399	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4847401	0.82[EUR][1000 genomes]
rs4847402	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs531358	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs531514	0.82[AMR][1000 genomes]
rs547866	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs555161	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs565919	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs612037	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs622608	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs624131	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs627779	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs637646	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs6541401	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6541404	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6682670	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6688230	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs687394	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs693737	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7418101	0.81[EUR][1000 genomes]
rs7513705	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs7517363	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7532195	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7532549	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7535628	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs7539307	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs7541687	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7553465	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7553916	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs797661	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs797668	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs797672	0.82[AMR][1000 genomes]
rs797675	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs797676	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs797680	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap]
rs9432459	0.81[EUR][1000 genomes]

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	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs12128131	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs12128131	RP4-717I23.3	cis	Thyroid	GTEx
rs12128131	DR1	cis	multi-tissue	Pritchard
rs12128131	RP4-717I23.3	cis	Whole Blood	GTEx
rs12128131	RP4-717I23.3	cis	Artery Aorta	GTEx
rs12128131	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs12128131	RP4-717I23.3	cis	lung	GTEx
rs12128131	DR1	Cis_1M	lymphoblastoid	RTeQTL
rs12128131	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs12128131	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs12128131	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs12128131	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs12128131	RP4-717I23.3	cis	Artery Tibial	GTEx
rs12128131	TMED5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93543800-93546400	Active TSS	Rectal Mucosa Donor 31	rectum
2	chr1:93543800-93546600	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr1:93543800-93546800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:93543800-93546800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:93543800-93546800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:93543800-93547400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:93543800-93547400	Active TSS	Fetal Kidney	kidney
8	chr1:93544000-93546400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:93544000-93546400	Active TSS	Fetal Muscle Trunk	muscle
10	chr1:93544000-93546400	Active TSS	Ovary	ovary
11	chr1:93544000-93546600	Active TSS	H9 Cell Line	embryonic stem cell
12	chr1:93544000-93546600	Active TSS	NHDF-Ad	bronchial
13	chr1:93544000-93546800	Active TSS	Primary T helper naive cells from peripheral blood	blood
14	chr1:93544000-93547000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:93544000-93547000	Active TSS	Fetal Stomach	stomach
16	chr1:93544000-93547000	Active TSS	K562	blood
17	chr1:93544000-93547200	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr1:93544000-93547200	Active TSS	A549	lung
19	chr1:93544000-93547200	Active TSS	HSMM	muscle
20	chr1:93544000-93547400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:93544000-93547400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:93544000-93547400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:93544000-93547600	Active TSS	H1 Cell Line	embryonic stem cell
24	chr1:93544000-93547600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:93544000-93548000	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr1:93544200-93546400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr1:93544200-93546400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr1:93544200-93546400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:93544200-93546400	Active TSS	Colonic Mucosa	Colon
30	chr1:93544200-93546400	Active TSS	Fetal Heart	heart
31	chr1:93544200-93546400	Active TSS	Psoas Muscle	Psoas
32	chr1:93544200-93546400	Active TSS	Right Ventricle	heart
33	chr1:93544200-93546600	Active TSS	Fetal Lung	lung
34	chr1:93544200-93546600	Active TSS	Fetal Muscle Leg	muscle
35	chr1:93544200-93546800	Active TSS	Primary hematopoietic stem cells short term culture	blood
36	chr1:93544200-93547000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
37	chr1:93544200-93547000	Active TSS	Hela-S3	cervix
38	chr1:93544200-93547000	Active TSS	HSMMtube	muscle
39	chr1:93544200-93547200	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr1:93544200-93547200	Active TSS	Fetal Intestine Large	intestine
41	chr1:93544200-93547200	Active TSS	Fetal Intestine Small	intestine
42	chr1:93544200-93547400	Active TSS	Brain Anterior Caudate	brain
43	chr1:93544200-93547600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:93544200-93548400	Active TSS	GM12878-XiMat	blood
45	chr1:93544400-93546400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:93544400-93546400	Active TSS	Muscle Satellite Cultured Cells	--
47	chr1:93544400-93546400	Active TSS	Cortex derived primary cultured neurospheres	brain
48	chr1:93544400-93546400	Active TSS	HUVEC	blood vessel
49	chr1:93544400-93546400	Active TSS	NH-A	brain
50	chr1:93544400-93546600	Active TSS	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links