Variant report

Variant	rs13105033
Chromosome Location	chr4:100533722-100533723
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:100527695..100530044-chr4:100533508..100536218,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10516445	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12639930	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12641768	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12647188	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs13112253	0.86[CEU][hapmap]
rs13126189	1.00[ASN][1000 genomes]
rs13130949	0.83[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs1352775	0.83[CEU][hapmap]
rs1491238	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2255119	0.85[LWK][hapmap];1.00[YRI][hapmap]
rs2306985	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805337	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828543	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699755	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6532825	0.95[ASN][1000 genomes]
rs6852647	0.88[ASN][1000 genomes]
rs7659550	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7698798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs881981	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs959247	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs991811	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879656	chr4:99976646-100533722	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv933074	chr4:100460951-100630600	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13105033	ADH1B	cis	cerebellum	SCAN
rs13105033	H2AFZ	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100507800-100533800	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr4:100516400-100546200	Strong transcription	Liver	Liver
3	chr4:100518800-100545200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr4:100522600-100545800	Strong transcription	Fetal Intestine Large	intestine
5	chr4:100524400-100534800	Strong transcription	Duodenum Mucosa	Duodenum
6	chr4:100526600-100535800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr4:100532200-100537000	Enhancers	Colon Smooth Muscle	Colon
8	chr4:100532400-100535200	Weak transcription	Fetal Intestine Small	intestine
9	chr4:100532600-100534800	Enhancers	Rectal Smooth Muscle	rectum
10	chr4:100532600-100535600	Weak transcription	Fetal Lung	lung
11	chr4:100532600-100535800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr4:100532600-100536400	Weak transcription	Fetal Muscle Leg	muscle
13	chr4:100532800-100533800	Weak transcription	HSMMtube	muscle
14	chr4:100532800-100534200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:100532800-100534200	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr4:100532800-100534400	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr4:100532800-100545200	Weak transcription	Aorta	Aorta
18	chr4:100533000-100533800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr4:100533400-100534200	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr4:100533400-100535000	Strong transcription	HepG2	liver
21	chr4:100533600-100534200	Enhancers	Psoas Muscle	Psoas
22	chr4:100533600-100534800	Enhancers	Pancreas	Pancrea

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