Variant report

Variant	rs6858032
Chromosome Location	chr4:100576326-100576327
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	NFIC	chr4:100576293-100577023	ECC-1	luminal epithelium:	n/a	n/a

Variant related genes	Relation type
ENSG00000248713	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10516446	0.88[ASN][1000 genomes]
rs11097667	0.81[ASN][1000 genomes]
rs11097669	0.81[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs12643429	0.88[ASN][1000 genomes]
rs12647527	0.81[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs12648918	0.86[ASN][1000 genomes]
rs1352777	0.86[ASN][1000 genomes]
rs17029135	0.81[ASN][1000 genomes]
rs17029142	0.81[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs17029165	0.86[ASN][1000 genomes]
rs17029251	0.81[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs17029277	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17029292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs2298747	0.86[ASN][1000 genomes]
rs2306984	0.86[ASN][1000 genomes]
rs3792681	0.81[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs3828542	0.88[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs4235440	0.86[ASN][1000 genomes]
rs4699384	0.97[ASN][1000 genomes]
rs4699385	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4699754	0.81[ASN][1000 genomes]
rs4699756	0.86[ASN][1000 genomes]
rs61074475	0.86[ASN][1000 genomes]
rs6817049	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6858700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72906793	0.81[ASN][1000 genomes]
rs72908710	0.86[ASN][1000 genomes]
rs72908716	0.86[ASN][1000 genomes]
rs72908742	0.95[ASN][1000 genomes]
rs871321	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs881980	0.81[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs931465	0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs956200	0.86[ASN][1000 genomes]

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
rs6858032	MANBA	cis	cerebellum	SCAN
rs6858032	EMCN	cis	parietal	SCAN
rs6858032	DNAJB14	cis	parietal	SCAN
rs6858032	H2AFZ	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:100567800-100579200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr4:100575000-100577200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr4:100575200-100577200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:100575400-100576600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
5	chr4:100575400-100576800	Enhancers	Fetal Brain Male	brain
6	chr4:100575800-100576600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr4:100575800-100576600	Active TSS	Right Ventricle	heart
8	chr4:100575800-100576800	Weak transcription	Left Ventricle	heart
9	chr4:100575800-100577000	Enhancers	Rectal Smooth Muscle	rectum
10	chr4:100575800-100577600	Enhancers	Hela-S3	cervix
11	chr4:100575800-100579800	Weak transcription	Right Atrium	heart
12	chr4:100576000-100576400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr4:100576000-100576400	Weak transcription	Aorta	Aorta
14	chr4:100576000-100576400	Weak transcription	Fetal Muscle Trunk	muscle
15	chr4:100576000-100576400	Active TSS	Fetal Muscle Leg	muscle
16	chr4:100576000-100576400	Weak transcription	Ovary	ovary
17	chr4:100576000-100576400	Active TSS	HSMMtube	muscle
18	chr4:100576000-100576600	Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr4:100576000-100577000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr4:100576000-100577000	Enhancers	HSMM	muscle
21	chr4:100576000-100577200	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr4:100576000-100579400	Weak transcription	Psoas Muscle	Psoas
23	chr4:100576200-100576400	Enhancers	Fetal Heart	heart
24	chr4:100576200-100576400	Enhancers	Fetal Lung	lung
25	chr4:100576200-100577000	Enhancers	Brain Anterior Caudate	brain
26	chr4:100576200-100577000	Enhancers	NH-A	brain
27	chr4:100576200-100577200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr4:100576200-100577200	Enhancers	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links