Variant report

Variant	rs960293
Chromosome Location	chr7:27774460-27774461
allele	C/G
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	EP300	chr7:27774202-27774621	K562	blood:	n/a	n/a
2	EP300	chr7:27773631-27774860	SK-N-SH	brain:	n/a	chr7:27773677-27773691
3	NR2F2	chr7:27774376-27775374	MCF-7	breast:	n/a	chr7:27774975-27774990
4	TBL1XR1	chr7:27774361-27774561	K562	blood:	n/a	n/a
5	FOXA2	chr7:27774290-27775520	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:27773133..27776591-chr7:27778404..27780614,3	MCF-7	breast:

Variant related genes	Relation type
TAX1BP1	TF binding region
ENSG00000106052	Chromatin interaction
ENSG00000229893	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11763499	0.93[EUR][1000 genomes]
rs11766320	0.92[EUR][1000 genomes]
rs17155666	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17155928	0.85[CHB][hapmap]
rs17611937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17685046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2051829	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2237337	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2285930	0.84[CEU][hapmap];0.85[CHB][hapmap]
rs2391486	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34369550	0.96[ASN][1000 genomes]
rs4722732	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4722733	0.98[ASN][1000 genomes]
rs4722739	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4722742	1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs55714615	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55738305	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56137979	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61538692	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62449631	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62454807	0.92[EUR][1000 genomes]
rs62454947	0.92[EUR][1000 genomes]
rs6462043	0.92[EUR][1000 genomes]
rs6950949	0.92[EUR][1000 genomes]
rs6957836	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6958125	0.92[EUR][1000 genomes]
rs6974060	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6974991	0.92[EUR][1000 genomes]
rs6978847	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs757964	0.96[ASN][1000 genomes]
rs7785305	0.95[ASN][1000 genomes]
rs7796790	0.93[ASN][1000 genomes]
rs7799957	0.80[CHB][hapmap]
rs7804317	0.95[ASN][1000 genomes]
rs7808062	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs960294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9638846	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9638847	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9639563	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9639564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][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	nsv949025	chr7:27578167-28075172	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats 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	26 gene(s)	inside rSNPs	diseases
2	nsv1028469	chr7:27767795-27939667	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs960293	TAX1BP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27760000-27778800	Weak transcription	HSMMtube	muscle
2	chr7:27770000-27778600	Weak transcription	Right Atrium	heart
3	chr7:27770600-27775400	Weak transcription	Pancreas	Pancrea
4	chr7:27771200-27775400	Weak transcription	Gastric	stomach
5	chr7:27772800-27778800	Enhancers	Fetal Intestine Small	intestine
6	chr7:27773000-27776000	Enhancers	HepG2	liver
7	chr7:27773600-27778600	Enhancers	Fetal Intestine Large	intestine
8	chr7:27773800-27774600	Enhancers	K562	blood
9	chr7:27774000-27774600	Enhancers	Stomach Mucosa	stomach
10	chr7:27774200-27774600	Enhancers	Small Intestine	intestine
11	chr7:27774200-27775200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr7:27774200-27775600	Enhancers	A549	lung
13	chr7:27774200-27775800	Enhancers	Liver	Liver
14	chr7:27774200-27775800	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr7:27774400-27774800	Enhancers	HUVEC	blood vessel
16	chr7:27774400-27775400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr7:27774400-27775600	Weak transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links