Variant report

Variant	rs2000869
Chromosome Location	chr11:120544871-120544872
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:120544382..120546404-chr11:120729409..120732174,2	K562	blood:

Variant related genes	Relation type
ENSG00000149403	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10736503	0.82[ASN][1000 genomes]
rs10790389	0.95[CHB][hapmap];0.91[ASN][1000 genomes]
rs10790395	0.95[CHB][hapmap];0.86[CHD][hapmap];0.94[ASN][1000 genomes]
rs10790396	0.94[ASN][1000 genomes]
rs10790397	0.93[ASN][1000 genomes]
rs10790398	0.95[CHB][hapmap];0.94[ASN][1000 genomes]
rs10790399	0.93[ASN][1000 genomes]
rs10892608	0.87[CHB][hapmap];0.92[ASN][1000 genomes]
rs10892609	0.95[CHB][hapmap];0.84[CHD][hapmap];0.94[ASN][1000 genomes]
rs10892612	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs11217950	0.95[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11217956	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11217967	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11217968	0.80[ASN][1000 genomes]
rs11217971	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs11820810	0.90[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12365194	0.80[ASN][1000 genomes]
rs12574186	0.95[CHB][hapmap];0.93[ASN][1000 genomes]
rs2000868	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs2000870	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35101469	0.92[ASN][1000 genomes]
rs4417279	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs7119539	0.80[ASN][1000 genomes]
rs7119655	0.80[ASN][1000 genomes]
rs7932158	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs7934734	0.81[ASN][1000 genomes]
rs7947520	0.91[CHB][hapmap];0.83[ASN][1000 genomes]

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	nsv468881	chr11:120446830-120551100	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv556476	chr11:120446830-120551100	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1054407	chr11:120535570-120630114	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1053607	chr11:120540795-120802006	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2000869	IL10RA	cis	cerebellum	SCAN
rs2000869	GRIK4	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120533200-120551800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr11:120538400-120545000	Weak transcription	Ovary	ovary
3	chr11:120538600-120551800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr11:120538600-120552000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:120543800-120547000	Enhancers	HepG2	liver
6	chr11:120544000-120546200	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr11:120544200-120547600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr11:120544400-120545400	Enhancers	Spleen	Spleen
9	chr11:120544400-120546000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr11:120544400-120547600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr11:120544400-120552200	Weak transcription	Brain Substantia Nigra	brain
12	chr11:120544600-120545000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr11:120544600-120545400	Enhancers	Duodenum Mucosa	Duodenum
14	chr11:120544600-120546600	Enhancers	Fetal Intestine Large	intestine
15	chr11:120544800-120547000	Enhancers	Fetal Intestine Small	intestine

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