Variant report

Variant	rs4889640
Chromosome Location	chr16:31264267-31264268
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:31224374..31227422-chr16:31262287..31264332,3	MCF-7	breast:
2	chr16:31250159..31252637-chr16:31262961..31264861,2	K562	blood:
3	chr16:31260386..31262455-chr16:31263713..31265453,2	MCF-7	breast:
4	chr16:31252663..31255593-chr16:31260299..31264872,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177238	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10438639	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1052352	0.82[GIH][hapmap];0.83[JPT][hapmap]
rs11150613	0.86[CHB][hapmap]
rs11150614	0.82[GIH][hapmap]
rs11150616	0.80[GIH][hapmap]
rs11574631	0.86[CHB][hapmap];0.80[GIH][hapmap]
rs11641624	0.87[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11645526	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11864632	0.96[CEU][hapmap];0.83[JPT][hapmap]
rs11865830	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12449089	0.81[ASN][1000 genomes]
rs12929077	0.96[CEU][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs13336592	0.92[CEU][hapmap]
rs17708638	0.83[CEU][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap]
rs1808430	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2011491	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2288005	0.82[GIH][hapmap];0.83[JPT][hapmap]
rs2359661	0.92[CHB][hapmap];0.85[CHD][hapmap];0.84[ASN][1000 genomes]
rs2735393	0.96[CEU][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs3087796	0.83[CHB][hapmap]
rs3764327	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3815801	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4077810	0.86[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.82[TSI][hapmap]
rs4447446	0.84[ASN][1000 genomes]
rs4459557	0.86[CHB][hapmap]
rs4561481	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4597342	0.86[CHB][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap]
rs4889537	0.96[CEU][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4889538	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4889633	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4889639	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4889644	0.81[EUR][1000 genomes]
rs60660286	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6565225	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7186832	0.96[CEU][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs7187143	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs7193943	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7196256	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7206295	0.86[CHB][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.87[TSI][hapmap]
rs741810	0.96[CEU][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs7499192	0.80[CEU][hapmap];0.92[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8044075	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8047985	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8048583	0.92[CEU][hapmap];0.92[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8051304	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8056505	0.96[CEU][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.84[TSI][hapmap]
rs8057320	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8060268	0.86[CHB][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap]
rs8062426	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs889549	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs889551	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929868	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9673519	0.88[CHB][hapmap]
rs9923270	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9938177	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[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	nsv431451	chr16:30682399-31340999	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
2	nsv1066073	chr16:31219071-31278572	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs4889640	ITGAX	cis	lymphoblastoid	seeQTL
rs4889640	RABEP2	cis	cerebellum	SCAN
rs4889640	MYST1	cis	parietal	SCAN
rs4889640	PYDC1	cis	Skin Sun Exposed Lower leg	GTEx
rs4889640	QPRT	cis	cerebellum	SCAN
rs4889640	YPEL3	cis	parietal	SCAN
rs4889640	FUS	cis	cerebellum	SCAN
rs4889640	ITGAM	cis	lymphoblastoid	seeQTL
rs4889640	ITGAM	cis	multi-tissue	Pritchard
rs4889640	ITGAX	cis	multi-tissue	Pritchard
rs4889640	CD19	cis	cerebellum	SCAN
rs4889640	TUFM	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31260400-31265000	Weak transcription	NHEK	skin
2	chr16:31261200-31264400	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr16:31261200-31264600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr16:31262800-31264400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr16:31262800-31265000	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr16:31262800-31265000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr16:31262800-31265200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr16:31262800-31271800	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr16:31263000-31265000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr16:31263000-31271000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr16:31263400-31268400	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr16:31264000-31265000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr16:31264000-31265000	Enhancers	K562	blood
14	chr16:31264200-31265000	Enhancers	Primary B cells from cord blood	blood
15	chr16:31264200-31265000	Enhancers	A549	lung
16	chr16:31264200-31265400	Enhancers	Fetal Intestine Large	intestine
17	chr16:31264200-31265600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr16:31264200-31268200	Enhancers	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links