Variant report

Variant	rs666432
Chromosome Location	chr11:120003533-120003534
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11217755	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs12418601	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs12421142	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2848728	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2851718	0.81[CEU][hapmap];0.86[JPT][hapmap]
rs35650539	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4938791	1.00[CEU][hapmap];0.95[JPT][hapmap]
rs547124	0.83[CEU][hapmap]
rs582071	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs604413	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61900474	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61900479	0.82[ASN][1000 genomes]
rs620602	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs626151	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs657898	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs659912	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs673292	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7949789	0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]

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	nsv1054057	chr11:119781953-120519770	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv541178	chr11:119781953-120519770	Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1050132	chr11:119976310-120010437	Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs666432	THY1	cis	cerebellum	SCAN
rs666432	C2CD2L	cis	cerebellum	SCAN
rs666432	ABCG4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:119999000-120006400	Enhancers	Placenta	Placenta
2	chr11:120000400-120008400	Weak transcription	Duodenum Mucosa	Duodenum
3	chr11:120000600-120006400	Weak transcription	Fetal Thymus	thymus
4	chr11:120001400-120005200	Weak transcription	Hela-S3	cervix
5	chr11:120001400-120007800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr11:120002000-120006000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr11:120002400-120003800	Enhancers	Pancreas	Pancrea
8	chr11:120002800-120004000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr11:120002800-120006200	Transcr. at gene 5' and 3'	NHEK	skin
10	chr11:120003200-120003600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr11:120003200-120003600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr11:120003200-120005200	Transcr. at gene 5' and 3'	HMEC	breast
13	chr11:120003200-120008200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr11:120003400-120004400	Active TSS	Esophagus	oesophagus

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links