Variant report

Variant	rs6843738
Chromosome Location	chr4:103936001-103936002
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:103929746..103932464-chr4:103934730..103936768,2	MCF-7	breast:
2	chr4:103935447..103937592-chr4:104011447..104014383,2	K562	blood:
3	chr4:103926723..103928662-chr4:103933638..103936624,2	K562	blood:
4	chr4:103934937..103936463-chr4:103938822..103940719,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10006474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10013062	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10516495	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MKK][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10516496	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11929841	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11946020	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13113099	0.84[GIH][hapmap];0.85[JPT][hapmap]
rs13149311	0.80[JPT][hapmap];0.82[MEX][hapmap];0.83[AMR][1000 genomes]
rs13150953	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13151569	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1481279	0.84[GIH][hapmap];0.86[JPT][hapmap]
rs223317	0.95[CEU][hapmap]
rs223331	0.95[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap]
rs223361	0.95[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap]
rs223366	0.89[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs223374	0.95[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap]
rs223401	0.81[CEU][hapmap]
rs2866416	1.00[CEU][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34475639	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4698875	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4698876	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699048	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6533039	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6816370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7437975	0.82[ASN][1000 genomes]
rs7665026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7674212	0.82[GIH][hapmap]
rs7691873	0.84[GIH][hapmap];0.86[JPT][hapmap]
rs9991335	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757946	chr4:103780705-104057321	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759270	chr4:103780705-104057321	ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv461598	chr4:103807720-103953389	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv594978	chr4:103807720-103953389	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv879684	chr4:103887561-103939894	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv3429917	chr4:103915319-104207455	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv830021	chr4:103934454-104100588	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6843738	KRT8P46	cis	lung	GTEx
rs6843738	MANBA	cis	multi-tissue	Pritchard
rs6843738	MANBA	Cis_1M	lymphoblastoid	RTeQTL
rs6843738	LRRC37A15P	cis	Thyroid	GTEx
rs6843738	CISD2	cis	cerebellum	SCAN
rs6843738	BDH2	Cis_1M	lymphoblastoid	RTeQTL
rs6843738	MANBA	cis	parietal	SCAN
rs6843738	MANBA	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103932600-103939600	Weak transcription	HepG2	liver
2	chr4:103933000-103939600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr4:103933000-103940000	Weak transcription	Right Atrium	heart
4	chr4:103933200-103939800	Weak transcription	NHLF	lung
5	chr4:103933200-103940400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr4:103933600-103939800	Weak transcription	NHDF-Ad	bronchial
7	chr4:103933800-103938400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr4:103934000-103939000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr4:103934000-103939200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr4:103934000-103939800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr4:103934000-103939800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr4:103934000-103939800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr4:103934000-103939800	Weak transcription	Psoas Muscle	Psoas
14	chr4:103934000-103939800	Weak transcription	NHEK	skin
15	chr4:103934200-103939600	Weak transcription	K562	blood
16	chr4:103934200-103939800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr4:103934200-103939800	Weak transcription	Adipose Nuclei	Adipose
18	chr4:103934200-103939800	Weak transcription	Brain Substantia Nigra	brain
19	chr4:103934200-103939800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr4:103934200-103940200	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr4:103934400-103939600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr4:103934400-103940000	Weak transcription	Colon Smooth Muscle	Colon
23	chr4:103934600-103938400	Weak transcription	Hela-S3	cervix
24	chr4:103934600-103939800	Weak transcription	Brain Anterior Caudate	brain
25	chr4:103935600-103939000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links