Variant report

Variant	rs7035466
Chromosome Location	chr9:98535990-98535991
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	chr9:98535314..98537899-chr9:98637650..98639305,2	K562	blood:
2	chr9:98534328..98536116-chr9:98636365..98638226,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175611	Chromatin interaction
ENSG00000182150	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs4742753	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4743316	1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4743317	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6478964	1.00[CEU][hapmap];0.90[CHB][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6478965	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7045260	0.86[AMR][1000 genomes];0.94[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	nsv893598	chr9:98508628-98645674	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv482884	chr9:98530027-98691937	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7035466	BARX1	cis	parietal	SCAN
rs7035466	SLC35D2	cis	parietal	SCAN
rs7035466	XPA	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98533000-98536000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr9:98533400-98536200	Enhancers	Fetal Stomach	stomach
3	chr9:98533800-98536000	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr9:98534200-98536200	Enhancers	Fetal Lung	lung
5	chr9:98534200-98539800	Weak transcription	Lung	lung
6	chr9:98534800-98539200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:98535000-98536000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
8	chr9:98535000-98536000	Enhancers	NHLF	lung
9	chr9:98535000-98536600	Enhancers	Fetal Kidney	kidney
10	chr9:98535200-98537800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr9:98535200-98539000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:98535400-98536000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr9:98535400-98536000	Enhancers	Ovary	ovary
14	chr9:98535400-98536000	Enhancers	HSMMtube	muscle
15	chr9:98535400-98536400	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr9:98535400-98537200	Weak transcription	Pancreas	Pancrea
17	chr9:98535400-98537400	Enhancers	HepG2	liver
18	chr9:98535400-98538600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr9:98535400-98550800	Weak transcription	Right Atrium	heart
20	chr9:98535600-98536000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
21	chr9:98535600-98536000	Weak transcription	Duodenum Mucosa	Duodenum
22	chr9:98535600-98537200	Weak transcription	Fetal Intestine Large	intestine
23	chr9:98535600-98537400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr9:98535600-98538600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr9:98535600-98539800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr9:98535600-98545800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr9:98535800-98536000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr9:98535800-98536400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links