Variant report

Variant	rs7678889
Chromosome Location	chr4:100586015-100586016
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:100582949..100584886-chr4:100585826..100588092,2	MCF-7	breast:
2	chr4:100578815..100580897-chr4:100583888..100586485,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1027223	0.93[ASN][1000 genomes]
rs10516445	0.83[CEU][hapmap]
rs10516455	0.93[ASN][1000 genomes]
rs1115721	0.93[ASN][1000 genomes]
rs11722443	0.88[ASN][1000 genomes]
rs11730739	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11936303	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12639747	0.82[JPT][hapmap]
rs12640222	0.87[ASN][1000 genomes]
rs12642668	0.81[ASN][1000 genomes]
rs12643245	0.88[ASN][1000 genomes]
rs12648843	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13111133	0.80[ASN][1000 genomes]
rs13111603	0.80[ASN][1000 genomes]
rs13112253	0.86[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13114983	0.82[ASN][1000 genomes]
rs13118288	0.90[ASN][1000 genomes]
rs13123629	0.90[ASN][1000 genomes]
rs13123690	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13124255	0.94[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs13130068	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13130949	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13150247	0.88[ASN][1000 genomes]
rs1352775	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1388295	0.90[ASN][1000 genomes]
rs1426734	0.80[ASN][1000 genomes]
rs1491240	0.82[JPT][hapmap]
rs1582793	0.83[ASN][1000 genomes]
rs1586756	0.93[ASN][1000 genomes]
rs1586757	0.94[ASN][1000 genomes]
rs17029269	0.82[ASN][1000 genomes]
rs17029387	0.88[ASN][1000 genomes]
rs1816197	0.89[ASN][1000 genomes]
rs1834659	0.80[ASN][1000 genomes]
rs1948353	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2306986	0.82[JPT][hapmap]
rs2866167	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35215295	0.93[ASN][1000 genomes]
rs36098323	0.92[ASN][1000 genomes]
rs3792683	0.82[JPT][hapmap]
rs61705069	0.86[ASN][1000 genomes]
rs66931934	0.82[ASN][1000 genomes]
rs6831328	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6832692	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6840719	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6852647	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71614607	0.93[ASN][1000 genomes]
rs7670607	0.94[CHB][hapmap];0.93[CHD][hapmap];0.89[ASN][1000 genomes]
rs7675468	0.82[JPT][hapmap]
rs7677213	0.91[EUR][1000 genomes]
rs7677594	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7678142	0.82[JPT][hapmap]
rs7688255	0.80[ASN][1000 genomes]
rs7691498	0.81[ASN][1000 genomes]
rs884276	0.82[JPT][hapmap]
rs958868	0.82[JPT][hapmap]
rs991811	0.83[CEU][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	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7678889	H2AFZ	cis	cerebellum	SCAN
rs7678889	ADH1B	cis	cerebellum	SCAN
rs7678889	MANBA	cis	parietal	SCAN
rs7678889	RARB	trans	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100580000-100600400	Weak transcription	Psoas Muscle	Psoas
2	chr4:100580600-100586600	Weak transcription	Stomach Smooth Muscle	stomach
3	chr4:100585600-100587400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr4:100585600-100588800	Enhancers	Fetal Lung	lung
5	chr4:100586000-100586200	Enhancers	Fetal Kidney	kidney
6	chr4:100586000-100586800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr4:100586000-100586800	Enhancers	Rectal Smooth Muscle	rectum
8	chr4:100586000-100587400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:100586000-100587400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr4:100586000-100588000	Enhancers	Ovary	ovary
11	chr4:100586000-100588200	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr4:100586000-100588200	Enhancers	Fetal Heart	heart

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