Variant report

Variant	rs12134420
Chromosome Location	chr1:85738308-85738309
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:85738169-85740047	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr1:85737298-85738796	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:85738277-85742976	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:85731137..85733599-chr1:85736126..85739884,4	MCF-7	breast:
2	chr1:85723639..85725384-chr1:85737240..85739229,2	MCF-7	breast:
3	chr1:85726071..85727906-chr1:85736264..85738614,2	K562	blood:

Variant related genes	Relation type
ENSG00000223653	TF binding region
ENSG00000162642	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10158486	1.00[ASW][hapmap];0.94[CEU][hapmap];0.83[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.92[MEX][hapmap];0.95[MKK][hapmap];0.96[TSI][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10493763	1.00[ASW][hapmap];0.94[CEU][hapmap];0.83[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.92[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10782544	0.84[ASN][1000 genomes]
rs11161562	0.87[ASN][1000 genomes]
rs12126112	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12126141	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12136214	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12729231	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12757160	0.83[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17382844	0.94[CEU][hapmap];0.82[CHB][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6698331	0.94[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71652692	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830459	chr1:85589585-85786311	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85725400-85741000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:85725800-85739400	Weak transcription	Aorta	Aorta
3	chr1:85726000-85741000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:85726000-85741400	Weak transcription	Gastric	stomach
5	chr1:85726200-85739800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:85727200-85741400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:85728200-85739400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:85728400-85738400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:85728600-85738800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:85728600-85739600	Strong transcription	Fetal Muscle Trunk	muscle
11	chr1:85728600-85739600	Strong transcription	HSMM	muscle
12	chr1:85728800-85739000	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:85728800-85739000	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr1:85728800-85739600	Strong transcription	Primary hematopoietic stem cells	blood
15	chr1:85729000-85739200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:85729200-85738400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:85729200-85738800	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr1:85729200-85739400	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr1:85729200-85739600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:85729400-85739200	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr1:85729600-85739000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr1:85729800-85739200	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:85729800-85739400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr1:85730000-85739000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:85730000-85739000	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr1:85730000-85739200	Strong transcription	HMEC	breast
27	chr1:85730200-85739200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:85730400-85739600	Weak transcription	Stomach Mucosa	stomach
29	chr1:85730600-85739200	Strong transcription	NH-A	brain
30	chr1:85730800-85739000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:85731000-85739200	Strong transcription	Hela-S3	cervix
32	chr1:85731200-85738600	Strong transcription	Osteobl	bone
33	chr1:85731200-85738800	Strong transcription	NHDF-Ad	bronchial
34	chr1:85731400-85738400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:85731800-85739000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr1:85732000-85738600	Strong transcription	NHEK	skin
37	chr1:85732000-85739000	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr1:85732200-85738400	Strong transcription	Fetal Muscle Leg	muscle
39	chr1:85732200-85738800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr1:85732600-85741000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:85732800-85739800	Strong transcription	K562	blood
42	chr1:85733400-85739000	Strong transcription	Primary T cells from cord blood	blood
43	chr1:85734200-85739000	Genic enhancers	Fetal Intestine Large	intestine
44	chr1:85734800-85740200	Weak transcription	Right Atrium	heart
45	chr1:85735000-85741400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr1:85735000-85741400	Weak transcription	Pancreas	Pancrea
47	chr1:85735400-85739000	Genic enhancers	Duodenum Mucosa	Duodenum
48	chr1:85735400-85740600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr1:85735600-85738800	Weak transcription	Psoas Muscle	Psoas
50	chr1:85735600-85739800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links