Variant report

Variant	rs17787966
Chromosome Location	chr11:47070425-47070426
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11039076	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11039122	0.89[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap]
rs1685404	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs2291443	0.96[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[ASN][1000 genomes]
rs2291444	0.96[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.83[ASN][1000 genomes]
rs7117404	1.00[LWK][hapmap]
rs7123635	0.82[AMR][1000 genomes]
rs7130812	0.90[GIH][hapmap]
rs752848	0.96[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs752850	0.96[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs901750	0.88[CEU][hapmap];0.94[CHB][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043108	chr11:47041565-47117248	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv312	chr11:47047247-47072397	Weak transcription Enhancers ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv508627	chr11:47052659-47084007	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv554206	chr11:47061100-47071897	Weak transcription Enhancers	TF binding region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs17787966	ATG13	cis	cerebellum	SCAN
rs17787966	C1QTNF4	cis	lymphoblastoid	seeQTL
rs17787966	NUP160	cis	cerebellum	SCAN
rs17787966	MADD	cis	parietal	SCAN
rs17787966	LRP4-AS1	cis	Nerve Tibial	GTEx
rs17787966	CTD-2384B9.1	cis	Nerve Tibial	GTEx
rs17787966	LRP4	cis	Nerve Tibial	GTEx
rs17787966	CKAP5	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47026800-47080200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr11:47053400-47077600	Weak transcription	Primary T cells from cord blood	blood
3	chr11:47055400-47077200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr11:47055600-47077800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr11:47056400-47073600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr11:47056600-47073800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr11:47057200-47074200	Weak transcription	Hela-S3	cervix
8	chr11:47058600-47074800	Weak transcription	Fetal Intestine Small	intestine
9	chr11:47061400-47082800	Weak transcription	Brain Angular Gyrus	brain
10	chr11:47064000-47077600	Weak transcription	Fetal Lung	lung
11	chr11:47065000-47079000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr11:47065200-47073000	Weak transcription	Fetal Stomach	stomach
13	chr11:47067000-47077200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr11:47068200-47079000	Weak transcription	Fetal Brain Male	brain
15	chr11:47068400-47092400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr11:47070200-47080000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr11:47070400-47079000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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

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