Variant report

Variant	rs2798352
Chromosome Location	chr1:47640756-47640757
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	CTCF	chr1:47640740-47640890	GM12871	blood:	n/a	n/a
2	NR3C1	chr1:47640730-47641234	A549	lung:	n/a	n/a
3	CTCF	chr1:47640700-47640850	HMEC	breast:	n/a	n/a
4	CTCF	chr1:47640680-47640830	AG09309	skin:	n/a	n/a
5	CTCF	chr1:47640583-47641650	SK-N-SH	brain:	n/a	chr1:47641189-47641207 chr1:47641184-47641205 chr1:47641194-47641202
6	POLR2A	chr1:47640629-47641329	Hela-S3	cervix:	n/a	n/a
7	CTCF	chr1:47640720-47640870	GM12873	blood:	n/a	n/a
8	SMC3	chr1:47639288-47641516	SK-N-SH	brain:	n/a	chr1:47639685-47639699
9	CTCF	chr1:47640720-47640870	HEEpiC	esophagus:	n/a	n/a
10	CTCF	chr1:47640660-47640810	GM12865	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:47639046..47642799-chr1:47643265..47647842,8	K562	blood:
2	chr1:47640366..47642048-chr1:47695486..47697663,2	K562	blood:
3	chr1:47639023..47641866-chr1:47695486..47697067,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PDZK1IP1-1	chr1:47640226-47640990	XLOC_000819

Variant related genes	Relation type
LINC00853	TF binding region
ENSG00000162367	Chromatin interaction
ENSG00000224805	Chromatin interaction
ENSG00000225506	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10789500	0.84[EUR][1000 genomes]
rs10789501	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10789503	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10890446	0.82[MEX][hapmap]
rs10890457	0.87[CEU][hapmap];0.90[TSI][hapmap]
rs10890460	0.87[CEU][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs10890462	0.81[EUR][1000 genomes]
rs10890464	0.87[CEU][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs10890465	0.82[EUR][1000 genomes]
rs10890466	0.83[EUR][1000 genomes]
rs10890467	0.83[EUR][1000 genomes]
rs10890468	0.84[EUR][1000 genomes]
rs10890470	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1110425	0.82[EUR][1000 genomes]
rs11211439	0.81[TSI][hapmap]
rs11211446	0.87[CEU][hapmap]
rs11211450	0.82[EUR][1000 genomes]
rs11211451	0.87[CEU][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs11211454	0.80[EUR][1000 genomes]
rs11211457	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs11211459	0.81[EUR][1000 genomes]
rs11211463	0.81[EUR][1000 genomes]
rs11211464	0.87[EUR][1000 genomes]
rs11211471	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11211472	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11211475	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12037014	0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs12042073	0.83[EUR][1000 genomes]
rs12046348	0.83[EUR][1000 genomes]
rs12046525	0.83[EUR][1000 genomes]
rs12124648	0.83[EUR][1000 genomes]
rs12564635	0.81[TSI][hapmap]
rs12734327	0.87[CEU][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs1847222	0.87[CEU][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs1847223	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs1847224	0.82[EUR][1000 genomes]
rs1967756	0.83[EUR][1000 genomes]
rs1967757	0.87[CEU][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs2016160	0.87[CEU][hapmap]
rs2208772	0.84[EUR][1000 genomes]
rs2224622	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2494248	0.92[CEU][hapmap];0.93[GIH][hapmap];0.81[EUR][1000 genomes]
rs2742079	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2798356	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2821082	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28462300	0.82[EUR][1000 genomes]
rs28796303	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3850876	0.84[EUR][1000 genomes]
rs4314923	0.82[EUR][1000 genomes]
rs4926785	0.87[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs4926786	0.81[EUR][1000 genomes]
rs4926787	0.81[EUR][1000 genomes]
rs4926788	0.81[EUR][1000 genomes]
rs4926789	0.81[EUR][1000 genomes]
rs4926791	0.81[EUR][1000 genomes]
rs4926792	0.81[EUR][1000 genomes]
rs4926793	0.87[CEU][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs4926797	0.82[EUR][1000 genomes]
rs4926804	0.82[EUR][1000 genomes]
rs4926805	0.81[EUR][1000 genomes]
rs4926809	0.82[EUR][1000 genomes]
rs4926826	0.82[EUR][1000 genomes]
rs4926869	0.82[EUR][1000 genomes]
rs4926918	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6588388	0.80[EUR][1000 genomes]
rs6664392	0.87[CEU][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs6664496	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs6675902	0.82[EUR][1000 genomes]
rs6690005	0.87[CEU][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs6693145	0.82[EUR][1000 genomes]
rs6701611	0.82[EUR][1000 genomes]
rs7512729	0.80[EUR][1000 genomes]
rs7519903	0.82[EUR][1000 genomes]
rs7522639	0.82[EUR][1000 genomes]
rs7526674	0.82[EUR][1000 genomes]
rs7540264	0.82[EUR][1000 genomes]
rs7545034	1.00[CHD][hapmap]
rs7545399	0.83[CEU][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap]
rs7547893	0.80[EUR][1000 genomes]
rs760440	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs760441	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs760442	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs911903	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs911909	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9633421	0.83[EUR][1000 genomes]
rs9793471	0.83[MEX][hapmap];0.88[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916813	chr1:47435635-47666179	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2798352	HECTD3	cis	cerebellum	SCAN
rs2798352	MOBKL2C	cis	cerebellum	SCAN
rs2798352	SPATA6	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47596400-47641000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:47638800-47644800	Weak transcription	Ovary	ovary
3	chr1:47639400-47641600	Enhancers	Fetal Lung	lung
4	chr1:47639800-47640800	Weak transcription	Liver	Liver
5	chr1:47640000-47644600	Weak transcription	Right Atrium	heart
6	chr1:47640400-47641200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:47640600-47640800	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr1:47640600-47640800	Enhancers	Brain Cingulate Gyrus	brain
9	chr1:47640600-47640800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:47640600-47641000	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr1:47640600-47641200	Enhancers	Fetal Stomach	stomach
12	chr1:47640600-47641400	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr1:47640600-47641400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:47640600-47641400	Enhancers	Hela-S3	cervix
15	chr1:47640600-47641600	Enhancers	Fetal Brain Female	brain
16	chr1:47640600-47641600	Enhancers	NHEK	skin
17	chr1:47640600-47641800	Enhancers	Brain Hippocampus Middle	brain
18	chr1:47640600-47641800	Enhancers	HMEC	breast
19	chr1:47640600-47643000	Enhancers	HepG2	liver

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