Variant report

Variant	rs34619
Chromosome Location	chr5:60465365-60465366
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:60463482..60466191-chr5:60507654..60510350,2	MCF-7	breast:
2	chr5:60464941..60466921-chr5:60605078..60607461,2	MCF-7	breast:
3	chr5:60454421..60471345-chr5:60622342..60633215,36	MCF-7	breast:
4	chr5:60457686..60461710-chr5:60461785..60466060,5	MCF-7	breast:
5	chr5:60464303..60466155-chr5:60475802..60477971,2	K562	blood:
6	chr5:60454193..60465680-chr5:60622262..60629761,38	MCF-7	breast:
7	chr5:60457400..60460151-chr5:60465192..60468109,3	MCF-7	breast:
8	chr5:60454738..60463245-chr5:60465333..60477980,25	K562	blood:
9	chr5:60464487..60466680-chr5:60468300..60471010,2	K562	blood:
10	chr5:60464643..60466155-chr5:60475802..60478493,2	K562	blood:
11	chr5:60463738..60466633-chr5:60467001..60468550,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NDUFAF2-3	chr5:60464189-60465734	NONHSAT101659

No data

Variant related genes	Relation type
ENSG00000188725	Chromatin interaction
ENSG00000251279	Chromatin interaction
ENSG00000130449	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10805374	0.81[EUR][1000 genomes]
rs10939879	0.84[EUR][1000 genomes]
rs10939881	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11739952	0.84[EUR][1000 genomes]
rs12516995	0.83[EUR][1000 genomes]
rs12517310	0.83[EUR][1000 genomes]
rs12518404	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12518792	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12652830	0.81[EUR][1000 genomes]
rs12653132	0.91[EUR][1000 genomes]
rs12655209	0.83[EUR][1000 genomes]
rs1382917	0.84[EUR][1000 genomes]
rs1460961	0.96[CEU][hapmap];0.92[CHB][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1471488	0.80[EUR][1000 genomes]
rs1479645	0.83[EUR][1000 genomes]
rs1526896	0.91[EUR][1000 genomes]
rs159535	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs159536	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs159537	0.84[YRI][hapmap]
rs159543	0.81[ASN][1000 genomes]
rs17419290	0.86[EUR][1000 genomes]
rs17444495	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1983484	0.90[EUR][1000 genomes]
rs2049579	0.90[EUR][1000 genomes]
rs28436304	0.84[EUR][1000 genomes]
rs2898309	0.81[EUR][1000 genomes]
rs34608	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34609	0.83[YRI][hapmap]
rs34617	0.83[YRI][hapmap]
rs34625	0.84[YRI][hapmap];0.81[AFR][1000 genomes]
rs4642318	0.84[EUR][1000 genomes]
rs4647052	0.83[EUR][1000 genomes]
rs4700402	0.81[EUR][1000 genomes]
rs4700404	0.84[EUR][1000 genomes]
rs4700407	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55738840	0.83[EUR][1000 genomes]
rs55814394	0.83[EUR][1000 genomes]
rs56025209	0.90[EUR][1000 genomes]
rs56031340	0.84[EUR][1000 genomes]
rs56284222	0.91[EUR][1000 genomes]
rs56350217	0.81[EUR][1000 genomes]
rs58646987	0.84[EUR][1000 genomes]
rs61017995	0.81[EUR][1000 genomes]
rs62365455	0.84[EUR][1000 genomes]
rs62365458	0.81[EUR][1000 genomes]
rs62367862	0.81[EUR][1000 genomes]
rs62367872	0.84[EUR][1000 genomes]
rs62367879	0.81[EUR][1000 genomes]
rs62367885	0.82[EUR][1000 genomes]
rs62367903	0.86[EUR][1000 genomes]
rs6449512	0.80[EUR][1000 genomes]
rs67490467	0.84[EUR][1000 genomes]
rs68104763	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs726824	0.84[EUR][1000 genomes]
rs72757187	0.84[EUR][1000 genomes]
rs72759206	0.84[EUR][1000 genomes]
rs72759215	0.91[EUR][1000 genomes]
rs7709522	0.84[EUR][1000 genomes]
rs7713481	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7714396	0.85[EUR][1000 genomes]
rs7723901	0.81[EUR][1000 genomes]
rs7734205	0.86[EUR][1000 genomes]
rs7737276	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs868791	0.81[EUR][1000 genomes]
rs888799	0.90[EUR][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	nsv949662	chr5:60047974-60488379	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh 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	nsv1034038	chr5:60375328-60607654	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs34619	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL
rs34619	ERCC8	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60460000-60469000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr5:60460000-60473000	Weak transcription	HSMM	muscle
3	chr5:60460400-60467200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:60460400-60470400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr5:60460400-60475000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:60463800-60472600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr5:60464800-60465600	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr5:60464800-60465600	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr5:60465200-60465400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:60465200-60465600	Enhancers	iPS-18 Cell Line	embryonic stem cell

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