Variant report

Variant	rs617950
Chromosome Location	chr11:105799746-105799747
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	GATA3	chr11:105799652-105800142	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr11:105799611-105800203	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000263371	TF binding region
GRIA4	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12573988	0.88[CHB][hapmap]
rs12574754	0.89[CHB][hapmap];0.81[AMR][1000 genomes]
rs12575492	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12577871	0.89[CHB][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1258586	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17104703	0.89[CHB][hapmap]
rs17104711	0.88[CHB][hapmap]
rs17104747	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1938912	0.89[CHB][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1938913	0.86[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2508467	0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs2509482	0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs2898230	0.89[CHB][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3758795	0.89[CHB][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3819079	0.88[CHB][hapmap]
rs4754137	0.89[CHB][hapmap]
rs4755119	0.89[CHB][hapmap]
rs4755120	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4755121	0.89[CHB][hapmap];0.80[ASN][1000 genomes]
rs502453	0.94[CEU][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs518639	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs535532	0.88[ASW][hapmap];0.83[CEU][hapmap];0.89[CHB][hapmap];0.88[GIH][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs538271	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs539153	1.00[ASW][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.85[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs552767	0.89[ASW][hapmap];0.94[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.84[LWK][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap]
rs585464	0.89[ASW][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.80[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.85[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs589904	1.00[ASW][hapmap];0.94[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.92[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs602098	0.89[ASW][hapmap];0.94[CEU][hapmap];0.89[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs609239	0.89[CHB][hapmap]
rs611352	0.94[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs652286	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66632571	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66698959	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs674307	0.94[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs675091	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs679914	0.86[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7116745	0.86[JPT][hapmap]
rs7945345	0.89[CHB][hapmap];0.81[AMR][1000 genomes];0.80[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	nsv832257	chr11:105662753-105817576	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs617950	C11orf70	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:105795000-105804600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr11:105795200-105800200	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr11:105795200-105806800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr11:105795400-105800000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr11:105795400-105805600	Weak transcription	Brain Substantia Nigra	brain
6	chr11:105795600-105800000	Weak transcription	Brain Hippocampus Middle	brain
7	chr11:105795600-105805600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr11:105796200-105800400	Weak transcription	Fetal Lung	lung
9	chr11:105797200-105806400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr11:105798000-105799800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr11:105799400-105800600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr11:105799400-105801200	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr11:105799400-105810200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr11:105799600-105800200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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