Variant report

Variant	rs3112200
Chromosome Location	chr2:39002637-39002638
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr2:39002042-39002685	K562	blood:	n/a	n/a
2	FOXA1	chr2:39002491-39002947	HepG2	liver:	n/a	n/a
3	HNF4A	chr2:39002417-39002952	HepG2	liver:	n/a	chr2:39002788-39002803

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:38974982..38979904-chr2:39002191..39014206,31	MCF-7	breast:
2	chr2:38975148..38982473-chr2:39000165..39007764,21	K562	blood:
3	chr2:38995074..38996747-chr2:39000854..39003003,2	MCF-7	breast:
4	chr2:39000825..39002881-chr2:39004010..39005901,3	MCF-7	breast:
5	chr2:38974922..38979621-chr2:38998984..39003561,8	K562	blood:
6	chr2:39001847..39003662-chr2:39018997..39021441,2	K562	blood:

No data

Variant related genes	Relation type
GEMIN6	TF binding region
ENSG00000232114	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000115875	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10173118	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10173240	0.89[CEU][hapmap];0.93[CHB][hapmap];0.88[EUR][1000 genomes]
rs10176932	0.94[CHB][hapmap];0.83[CHD][hapmap]
rs10197412	0.89[CEU][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs10865143	0.92[CEU][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10865144	0.88[EUR][1000 genomes]
rs11124646	0.94[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap]
rs11694383	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11889280	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12465043	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12468732	0.83[ASN][1000 genomes]
rs12469681	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12472454	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12473036	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12477252	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12618118	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12621103	0.80[ASW][hapmap];0.88[LWK][hapmap]
rs12712621	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs12712622	0.80[EUR][1000 genomes]
rs12991609	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12996194	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13011522	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13014136	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13024811	0.80[ASW][hapmap];0.83[LWK][hapmap]
rs13029406	0.89[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13383541	0.89[CEU][hapmap];0.94[CHB][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13411868	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13417196	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1529625	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs1530852	0.96[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1530853	0.92[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1979142	0.89[CEU][hapmap];0.94[CHB][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1997377	0.88[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap]
rs2037875	0.89[CEU][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs2272445	0.94[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs2373473	0.90[JPT][hapmap]
rs3099940	0.90[JPT][hapmap]
rs3099941	0.90[JPT][hapmap]
rs3099943	1.00[JPT][hapmap]
rs3099945	1.00[JPT][hapmap]
rs3099952	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3099960	0.97[ASN][1000 genomes]
rs3099965	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3099985	0.81[EUR][1000 genomes]
rs3099987	0.81[EUR][1000 genomes]
rs3099988	0.80[EUR][1000 genomes]
rs3099991	0.81[EUR][1000 genomes]
rs3112140	0.88[EUR][1000 genomes]
rs3112198	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3112205	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112209	0.92[ASN][1000 genomes]
rs3112210	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3112215	0.88[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs3112216	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3134628	0.80[ASW][hapmap];0.83[LWK][hapmap]
rs3770681	0.94[CHB][hapmap];0.87[GIH][hapmap]
rs4602206	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4630748	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4670894	0.86[ASN][1000 genomes]
rs4670897	0.88[EUR][1000 genomes]
rs56393601	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60012208	0.81[EUR][1000 genomes]
rs62144837	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6544175	0.95[ASN][1000 genomes]
rs6715866	0.92[CEU][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6728394	0.94[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap]
rs6746818	0.92[CEU][hapmap]
rs6753251	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6756847	0.94[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap]
rs7419616	0.92[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7419838	0.92[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7589162	0.81[CEU][hapmap];0.94[CHB][hapmap];0.81[EUR][1000 genomes]
rs7603676	0.94[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	esv1798055	chr2:38955865-39039504	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
4	nsv1014616	chr2:38985472-39022893	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3112200	DHX57	cis	cerebellum	SCAN
rs3112200	DHX57	cis	parietal	SCAN
rs3112200	SFRS7	Cis_1M	lymphoblastoid	RTeQTL
rs3112200	DHX57	cis	multi-tissue	Pritchard
rs3112200	MORN2	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38979200-39005000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:38994600-39004600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:38999200-39003600	Weak transcription	Placenta	Placenta
4	chr2:38999400-39004600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:38999400-39004600	Weak transcription	A549	lung
6	chr2:39000000-39004800	Weak transcription	Fetal Intestine Small	intestine
7	chr2:39002200-39003800	Flanking Active TSS	HepG2	liver
8	chr2:39002600-39003600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:39002600-39004600	Weak transcription	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links