Variant report

Variant	rs1860302
Chromosome Location	chr17:19914399-19914400
allele	A/T
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	IRF1	chr17:19913352-19914765	K562	blood:	n/a	chr17:19913823-19913839
2	CTCF	chr17:19911508-19914638	A549	lung:	n/a	chr17:19912622-19912631 chr17:19912985-19912998 chr17:19912998-19913011 chr17:19912617-19912633 chr17:19912019-19912028 chr17:19912619-19912629 chr17:19912616-19912634
3	GATA1	chr17:19912265-19914771	PBDE	blood:	n/a	chr17:19913659-19913676 chr17:19912495-19912503 chr17:19912493-19912505
4	ARID3A	chr17:19913458-19914684	K562	blood:	n/a	n/a
5	CUX1	chr17:19913446-19914407	K562	blood:	n/a	n/a
6	EP300	chr17:19913467-19914553	K562	blood:	n/a	n/a
7	ZNF274	chr17:19913137-19914410	K562	blood:	n/a	n/a
8	POLR2A	chr17:19912149-19914655	PBDE	blood:	n/a	n/a
9	HCFC1	chr17:19911771-19914635	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:19881019..19882535-chr17:19912703..19915442,2	K562	blood:
2	chr17:19913353..19915145-chr17:20008243..20011168,2	K562	blood:

Variant related genes	Relation type
ENSG00000261033	TF binding region
ENSG00000108599	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10083856	0.81[AMR][1000 genomes]
rs1034904	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11204421	0.84[ASN][1000 genomes]
rs11867585	0.92[JPT][hapmap]
rs11871651	0.81[AMR][1000 genomes]
rs119672	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs1479129	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs1638525	0.86[CHB][hapmap]
rs169412	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs16960644	0.84[ASN][1000 genomes]
rs175922	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs203450	0.94[CHB][hapmap]
rs203457	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs203458	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs203460	0.94[CHB][hapmap]
rs203462	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs203465	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs203466	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs203477	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs203479	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs203481	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs2042046	0.85[JPT][hapmap]
rs2108978	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs2108979	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2108980	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28807825	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34291370	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35003563	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs36034566	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3862152	0.83[AMR][1000 genomes]
rs3888318	0.83[AMR][1000 genomes]
rs3909258	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs397969	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs4005937	0.83[AMR][1000 genomes]
rs4479308	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4479309	0.80[AMR][1000 genomes]
rs4570919	0.80[AMR][1000 genomes]
rs4924801	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4924803	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4924806	0.80[AMR][1000 genomes]
rs4925060	0.87[CHB][hapmap]
rs4925065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925066	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925067	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925069	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4925072	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs4925073	0.82[AMR][1000 genomes]
rs4925077	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4925081	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs56142708	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62067555	0.80[AMR][1000 genomes]
rs7207625	0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs7208025	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs7208365	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs7208635	0.80[AMR][1000 genomes]
rs7209734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7211535	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7215514	0.83[ASN][1000 genomes]
rs7218708	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7222403	0.94[CHB][hapmap]
rs7223305	0.80[AMR][1000 genomes]
rs8065337	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8067545	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs850623	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs860335	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs888423	1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes]
rs918227	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs918228	0.80[AMR][1000 genomes]
rs9889743	0.81[AMR][1000 genomes]
rs9891739	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9897246	0.83[AMR][1000 genomes]
rs9906625	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9907788	0.82[AMR][1000 genomes]
rs9909009	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9915758	0.83[AMR][1000 genomes]
rs9916675	0.85[ASN][1000 genomes]
rs9944451	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv907869	chr17:19795774-19926836	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv833394	chr17:19827714-19999577	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv907870	chr17:19871922-20001612	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	esv3382860	chr17:19894909-19918588	Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	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
rs1860302	AKAP10	cis	multi-tissue	Pritchard
rs1860302	AKAP10	cis	Lymphoblastoid	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19911800-19914600	Active TSS	Brain Angular Gyrus	brain
2	chr17:19912000-19914600	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr17:19912000-19914600	Active TSS	Ovary	ovary
4	chr17:19912200-19914400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr17:19912200-19914600	Active TSS	Brain Hippocampus Middle	brain
6	chr17:19912200-19916200	Active TSS	K562	blood
7	chr17:19913600-19914400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr17:19913600-19914600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr17:19913800-19919400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr17:19913800-19921200	Weak transcription	Aorta	Aorta
11	chr17:19914000-19914400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
12	chr17:19914000-19914600	Flanking Active TSS	Brain Anterior Caudate	brain
13	chr17:19914000-19914600	Flanking Active TSS	A549	lung
14	chr17:19914000-19915200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr17:19914200-19914400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
16	chr17:19914200-19914400	Active TSS	Primary hematopoietic stem cells short term culture	blood
17	chr17:19914200-19914400	Enhancers	Pancreatic Islets	Pancreatic Islet
18	chr17:19914200-19914600	Active TSS	Brain Cingulate Gyrus	brain
19	chr17:19914200-19914600	Enhancers	Brain Substantia Nigra	brain
20	chr17:19914200-19915200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr17:19914200-19925000	Weak transcription	Adipose Nuclei	Adipose

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