Variant report

Variant	rs13392540
Chromosome Location	chr2:209128814-209128815
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:208393863..208396191-chr2:209128319..209130637,2	K562	blood:
2	chr2:209123964..209126958-chr2:209128019..209130689,2	K562	blood:
3	chr2:209128359..209130743-chr2:209169171..209171063,2	K562	blood:
4	chr2:209116323..209122695-chr2:209127326..209132568,14	K562	blood:
5	chr2:209116323..209123332-chr2:209127326..209134005,17	K562	blood:

Variant related genes	Relation type
ENSG00000223725	Chromatin interaction
ENSG00000138413	Chromatin interaction
ENSG00000231908	Chromatin interaction
ENSG00000118260	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10173938	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10174541	0.86[EUR][1000 genomes]
rs10175739	0.82[CHB][hapmap]
rs10176626	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10182087	0.84[CHB][hapmap];0.90[YRI][hapmap]
rs10186350	0.88[EUR][1000 genomes]
rs10186531	0.86[CHB][hapmap]
rs10189031	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10194539	0.86[EUR][1000 genomes]
rs10198535	0.88[EUR][1000 genomes]
rs10208191	0.86[CHB][hapmap]
rs10208295	0.86[CHB][hapmap]
rs10210393	0.86[CHB][hapmap]
rs10497897	0.86[EUR][1000 genomes]
rs10497898	0.86[EUR][1000 genomes]
rs10932256	0.86[CHB][hapmap]
rs10932259	0.86[CHB][hapmap]
rs10932260	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11898653	0.84[EUR][1000 genomes]
rs11901959	0.86[EUR][1000 genomes]
rs12185709	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12475932	0.88[CEU][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12623816	0.86[CHB][hapmap]
rs12694100	0.82[AMR][1000 genomes]
rs12694104	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12694109	0.86[CHB][hapmap]
rs13395304	0.88[EUR][1000 genomes]
rs13407897	0.86[EUR][1000 genomes]
rs13412043	0.86[EUR][1000 genomes]
rs1437414	0.86[CHB][hapmap]
rs1584200	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1595329	0.82[CHB][hapmap]
rs16840798	0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs16840864	0.86[CHB][hapmap]
rs16841092	0.86[CHB][hapmap]
rs16841231	0.86[CHB][hapmap]
rs16841233	0.86[CHB][hapmap]
rs16841234	0.84[CHB][hapmap]
rs1866044	0.86[CHB][hapmap]
rs1866045	0.86[CHB][hapmap]
rs1898436	0.86[CHB][hapmap]
rs1900239	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2304545	0.81[AMR][1000 genomes]
rs2363465	0.90[EUR][1000 genomes]
rs2363466	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2363468	0.86[CHB][hapmap]
rs35444703	0.82[YRI][hapmap]
rs3856350	0.86[CHB][hapmap];0.90[YRI][hapmap]
rs4462735	0.86[CHB][hapmap];0.82[YRI][hapmap]
rs4673391	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4673393	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4675748	0.86[CHB][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4675750	0.86[CHB][hapmap]
rs4675751	0.86[CHB][hapmap];0.88[EUR][1000 genomes]
rs56154808	0.91[ASN][1000 genomes]
rs66887797	0.88[EUR][1000 genomes]
rs6713477	0.86[CHB][hapmap]
rs6724208	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6725932	0.86[CHB][hapmap]
rs6736599	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6742461	0.86[CHB][hapmap]
rs67669827	0.86[EUR][1000 genomes]
rs73056463	0.86[EUR][1000 genomes]
rs7557303	0.86[EUR][1000 genomes]
rs7583022	0.86[CHB][hapmap];0.82[YRI][hapmap]
rs7587752	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9288392	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs959660	0.86[CHB][hapmap];0.90[YRI][hapmap]
rs962595	0.86[CHB][hapmap]
rs9646839	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010531	chr2:208610639-209176782	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv536130	chr2:208610639-209176782	Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS 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	40 gene(s)	inside rSNPs	diseases
4	nsv834517	chr2:209006797-209170269	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv584297	chr2:209020181-209316760	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:209120800-209129800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr2:209121200-209129600	Weak transcription	Left Ventricle	heart
3	chr2:209122200-209129600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr2:209122400-209129600	Weak transcription	Brain Substantia Nigra	brain
5	chr2:209122600-209129400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr2:209122600-209129600	Weak transcription	Brain Angular Gyrus	brain
7	chr2:209122800-209129600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr2:209122800-209129600	Weak transcription	Fetal Intestine Small	intestine
9	chr2:209122800-209129600	Weak transcription	Fetal Lung	lung
10	chr2:209123200-209129800	Weak transcription	Fetal Heart	heart
11	chr2:209127600-209129600	Weak transcription	Primary T cells from cord blood	blood
12	chr2:209128600-209129600	Enhancers	Dnd41	blood
13	chr2:209128800-209129600	Enhancers	HepG2	liver
14	chr2:209128800-209129800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr2:209128800-209129800	Enhancers	NHDF-Ad	bronchial

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links