Variant report

Variant	rs888822
Chromosome Location	chr5:80253321-80253322
allele	A/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	GATA3	chr5:80252722-80253558	MCF-7	breast:	n/a	n/a
2	JUND	chr5:80252638-80253346	H1-hESC	embryonic stem cell:	n/a	chr5:80253057-80253069 chr5:80253232-80253244
3	ZNF143	chr5:80253039-80253396	H1-hESC	embryonic stem cell:	n/a	n/a
4	GATA3	chr5:80252709-80253424	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
RASGRF2	TF binding region
ENSG00000251450	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10491488	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10491490	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12522495	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12653956	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2015661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs66484258	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6893705	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs888823	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv598747	chr5:79996632-80322712	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1016100	chr5:80023679-80254194	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1021784	chr5:80023679-80313586	ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv537787	chr5:80023679-80313586	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv830358	chr5:80197105-80358920	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs888822	XRCC4	cis	cerebellum	SCAN
rs888822	RASGRF2	cis	cerebellum	SCAN
rs888822	AP3B1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80249000-80255000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:80251000-80253800	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr5:80251600-80255800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:80251800-80253400	Bivalent Enhancer	Brain Germinal Matrix	brain
5	chr5:80252000-80254000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:80252200-80253400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr5:80252200-80254000	Enhancers	Primary T cells from cord blood	blood
8	chr5:80252400-80253400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:80252400-80253600	Enhancers	HepG2	liver
10	chr5:80252400-80254000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr5:80252400-80254000	Enhancers	H1 Cell Line	embryonic stem cell
12	chr5:80252400-80255600	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr5:80252400-80255600	Weak transcription	Ovary	ovary
14	chr5:80252600-80254000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:80252600-80255400	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr5:80252800-80255600	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr5:80253000-80253400	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr5:80253000-80255000	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr5:80253000-80255200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr5:80253000-80255200	Weak transcription	Brain Substantia Nigra	brain
21	chr5:80253000-80255200	Enhancers	Thymus	Thymus
22	chr5:80253000-80255400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
23	chr5:80253200-80253400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr5:80253200-80253400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr5:80253200-80254000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr5:80253200-80255400	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr5:80253200-80255600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr5:80253200-80256000	Bivalent Enhancer	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links