Variant report

Variant	rs376875
Chromosome Location	chr6:118611592-118611593
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11758375	0.82[CHB][hapmap]
rs11968293	0.88[CHB][hapmap];0.83[ASN][1000 genomes]
rs12212582	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1572226	0.88[CHB][hapmap];0.82[CHD][hapmap];0.83[ASN][1000 genomes]
rs1690662	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1874081	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1874082	0.83[ASN][1000 genomes]
rs188181	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs190756	0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs1923282	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs281861	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs281864	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs281867	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.92[YRI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs281868	0.94[CHB][hapmap];0.90[CHD][hapmap];0.83[MEX][hapmap]
rs283040	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs283042	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs283044	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs283045	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs283046	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs283047	0.81[ASN][1000 genomes]
rs283049	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs283050	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs283051	0.81[ASN][1000 genomes]
rs283057	0.93[ASN][1000 genomes]
rs283061	0.80[ASN][1000 genomes]
rs283062	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.94[ASN][1000 genomes]
rs283066	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs283067	0.81[ASN][1000 genomes]
rs283077	0.94[CHB][hapmap]
rs283080	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs283081	0.94[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.92[YRI][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs283082	0.83[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs283084	0.96[CEU][hapmap];0.94[CHB][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs283085	0.96[CEU][hapmap];0.94[CHB][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs283086	0.92[CEU][hapmap];0.94[CHB][hapmap];0.81[YRI][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs283087	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs283088	0.92[CEU][hapmap];0.94[CHB][hapmap];0.85[EUR][1000 genomes]
rs283091	0.88[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap];0.85[EUR][1000 genomes]
rs369383	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs372237	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.92[YRI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs387266	0.83[ASN][1000 genomes]
rs387945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs397445	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs399844	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs413876	0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs414091	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs419592	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs422268	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs422833	0.96[CEU][hapmap];0.94[CHB][hapmap];0.92[YRI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs431115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs445099	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs445566	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs447193	0.92[CEU][hapmap];0.94[CHB][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs450093	0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs4946333	0.94[CHB][hapmap];0.90[CHD][hapmap];0.83[MEX][hapmap]
rs4946336	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6912208	0.88[CHB][hapmap]
rs6927800	0.82[CHB][hapmap]
rs731695	0.82[CHB][hapmap]
rs7452622	0.81[CHB][hapmap]
rs7749263	0.82[CHB][hapmap]
rs89107	0.94[CHB][hapmap]
rs927348	0.82[CHB][hapmap]
rs9401060	0.94[CHB][hapmap];0.89[CHD][hapmap];0.83[MEX][hapmap]
rs9489327	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530526	chr6:118027339-118718476	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv532051	chr6:118551027-119044197	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1020463	chr6:118593028-119146363	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs376875	C6orf204	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:118606600-118613400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr6:118607600-118614000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr6:118607600-118616000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr6:118607600-118617000	Weak transcription	Fetal Muscle Leg	muscle
5	chr6:118608200-118613400	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr6:118608400-118613400	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr6:118608400-118613400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr6:118608600-118612800	Weak transcription	Colon Smooth Muscle	Colon
9	chr6:118609000-118616400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr6:118609400-118612600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr6:118609800-118616600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:118610000-118614800	Weak transcription	Aorta	Aorta
13	chr6:118610200-118617200	Weak transcription	Left Ventricle	heart
14	chr6:118611200-118612400	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links