Variant report

Variant	rs769238
Chromosome Location	chr4:122744942-122744943
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:122744374..122745052-chr6:111136551..111137493,2	Hela-S3	cervix:
2	chr4:122743728..122745720-chr4:123072564..123074276,2	MCF-7	breast:
3	chr4:122730694..122733208-chr4:122742795..122745639,3	MCF-7	breast:
4	chr4:122743665..122745647-chr4:122789959..122792844,2	K562	blood:
5	chr4:122743937..122745709-chr4:122789073..122792833,3	MCF-7	breast:
6	chr4:122719927..122724442-chr4:122741540..122746604,11	MCF-7	breast:
7	chr4:122722789..122724421-chr4:122743647..122745561,2	MCF-7	breast:
8	chr14:34419446..34420192-chr4:122744900..122745700,2	Hela-S3	cervix:
9	chr4:122743419..122745075-chr4:122767159..122769948,2	MCF-7	breast:
10	chr4:122744479..122745074-chr6:26216433..26217061,2	Hela-S3	cervix:
11	chr4:122743548..122747768-chr4:122748127..122751699,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000123737	Chromatin interaction
ENSG00000138686	Chromatin interaction
ENSG00000155111	Chromatin interaction
ENSG00000187990	Chromatin interaction
ENSG00000129521	Chromatin interaction
ENSG00000261501	Chromatin interaction
ENSG00000138688	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11098645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11098646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11098648	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11731570	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11731917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12502635	0.86[CHB][hapmap]
rs12512876	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12650359	0.86[CHB][hapmap]
rs1396080	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1507994	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1507995	0.91[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17452156	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2063165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2071486	0.91[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2221628	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3217753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3217771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3217773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3217780	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3828485	0.87[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3924987	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4077102	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4516739	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56077950	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56159666	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56311153	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58649165	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61217486	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6534323	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67772833	0.95[EUR][1000 genomes]
rs6815790	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6821305	0.88[ASN][1000 genomes]
rs6823818	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6824258	0.86[CHB][hapmap]
rs6826506	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6838153	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6855269	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72680779	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7660548	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7686084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7686200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7691955	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs769246	0.92[EUR][1000 genomes]
rs7699776	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9684587	0.97[EUR][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	nsv817261	chr4:122085173-123020068	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic 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 target site	30 gene(s)	inside rSNPs	diseases
2	nsv997539	chr4:122544104-123274266	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv530157	chr4:122557302-123248756	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs769238	EXOSC9	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:122742600-122745400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr4:122742600-122745600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr4:122742800-122745600	Active TSS	Thymus	Thymus
4	chr4:122742800-122745600	Active TSS	NHLF	lung
5	chr4:122743400-122745600	Active TSS	H1 Cell Line	embryonic stem cell
6	chr4:122743400-122745600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr4:122743400-122745600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr4:122743400-122745600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr4:122743400-122745600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:122743400-122745800	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr4:122743600-122745000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
12	chr4:122743600-122745400	Active TSS	HSMM	muscle
13	chr4:122743600-122745600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr4:122743600-122745600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
15	chr4:122743600-122745600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr4:122743600-122745600	Active TSS	Fetal Intestine Small	intestine
17	chr4:122743600-122745600	Active TSS	Hela-S3	cervix
18	chr4:122743600-122745800	Active TSS	Fetal Intestine Large	intestine
19	chr4:122743600-122745800	Active TSS	NHDF-Ad	bronchial
20	chr4:122743800-122745000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
21	chr4:122743800-122745000	Bivalent/Poised TSS	HepG2	liver
22	chr4:122743800-122745400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:122743800-122745400	Active TSS	HUES64 Cell Line	embryonic stem cell
24	chr4:122743800-122745400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr4:122743800-122745400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr4:122743800-122745400	Active TSS	Osteobl	bone
27	chr4:122743800-122745600	Active TSS	H9 Cell Line	embryonic stem cell
28	chr4:122743800-122745600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr4:122743800-122745600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr4:122743800-122745600	Active TSS	HSMMtube	muscle
31	chr4:122743800-122745800	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr4:122743800-122745800	Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr4:122743800-122745800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr4:122743800-122745800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr4:122743800-122745800	Active TSS	GM12878-XiMat	blood
36	chr4:122744000-122745000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
37	chr4:122744000-122745000	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr4:122744000-122745000	Flanking Active TSS	Liver	Liver
39	chr4:122744000-122745400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr4:122744000-122745400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr4:122744000-122745400	Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr4:122744000-122745400	Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr4:122744000-122745400	Active TSS	Muscle Satellite Cultured Cells	--
44	chr4:122744000-122745600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr4:122744000-122745600	Active TSS	iPS-15b Cell Line	embryonic stem cell
46	chr4:122744000-122745600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
47	chr4:122744000-122745600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr4:122744000-122745600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr4:122744000-122745600	Active TSS	Fetal Heart	heart
50	chr4:122744000-122745600	Active TSS	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links