Variant report

Variant	rs34973
Chromosome Location	chr5:80343441-80343442
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10942941	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1102241	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11746440	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11750527	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs153227	0.90[CHB][hapmap];0.89[JPT][hapmap];0.84[ASN][1000 genomes]
rs252585	0.85[GIH][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs26418	0.81[CHB][hapmap]
rs26900	0.83[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs26907	1.00[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.90[ASN][1000 genomes]
rs34901966	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs404361	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs422765	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs435707	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs439994	1.00[CEU][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs440583	0.85[CEU][hapmap];0.81[GIH][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs457638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs547145	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55727953	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55781224	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55802238	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61424809	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][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	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	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
3	nsv830360	chr5:80283278-80446040	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80319600-80374200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr5:80332800-80343800	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr5:80337200-80368600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr5:80337800-80355800	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr5:80338200-80370600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr5:80338200-80376200	Weak transcription	NHLF	lung
7	chr5:80338400-80345400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr5:80339200-80368600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr5:80339600-80346400	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr5:80339800-80355600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr5:80339800-80374200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr5:80340200-80345400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr5:80340400-80346000	Enhancers	Brain Substantia Nigra	brain
14	chr5:80340800-80344600	Enhancers	Brain Hippocampus Middle	brain
15	chr5:80341200-80348000	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr5:80341200-80356000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr5:80341400-80357400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr5:80341400-80360000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr5:80341800-80343600	Weak transcription	Brain Anterior Caudate	brain
20	chr5:80342000-80343600	Enhancers	Brain Angular Gyrus	brain
21	chr5:80342200-80344600	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr5:80342600-80344400	Enhancers	Brain Cingulate Gyrus	brain
23	chr5:80342800-80343800	Genic enhancers	HepG2	liver
24	chr5:80343000-80344000	Strong transcription	Primary T cells from cord blood	blood
25	chr5:80343200-80343800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr5:80343200-80366000	Weak transcription	Adipose Nuclei	Adipose
27	chr5:80343200-80394400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr5:80343400-80343800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr5:80343400-80347200	Weak transcription	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links