Variant report

Variant	rs8110247
Chromosome Location	chr19:52010404-52010405
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	GATA1	chr19:52009384-52012121	K562	blood:	n/a	chr19:52011791-52011801 chr19:52011555-52011562 chr19:52011553-52011562 chr19:52011177-52011187
2	TBL1XR1	chr19:52010306-52011708	K562	blood:	n/a	n/a
3	CBX3	chr19:52010361-52012240	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:52009466..52011500-chr19:52096366..52099744,3	K562	blood:
2	chr19:52004923..52007446-chr19:52009404..52012427,3	K562	blood:

Variant related genes	Relation type
SIGLEC27P	TF binding region
ENSG00000268839	TF binding region
ENSG00000254521	Chromatin interaction
ENSG00000269388	Chromatin interaction
ENSG00000167765	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10402495	1.00[ASN][1000 genomes]
rs10419489	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10421023	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10421468	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12461323	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12461345	0.97[ASN][1000 genomes]
rs12463300	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs13343377	0.94[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1551557	0.81[ASW][hapmap]
rs16982740	0.87[ASW][hapmap]
rs16982743	0.82[ASW][hapmap]
rs2034889	0.95[ASN][1000 genomes]
rs2034891	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs2864097	0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3810105	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs62116175	0.97[ASN][1000 genomes]
rs62116177	0.97[ASN][1000 genomes]
rs62116178	1.00[ASN][1000 genomes]
rs62116179	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6509545	0.82[ASN][1000 genomes]
rs7246846	0.94[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8106176	0.83[ASN][1000 genomes]
rs8106598	0.84[CHD][hapmap]
rs8113414	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9304717	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs962129	0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs962130	0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9676254	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9676256	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9676266	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9676272	0.93[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]

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	nsv1066308	chr19:51680133-52103974	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv544049	chr19:51680133-52103974	Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	nsv544051	chr19:51944903-52147459	Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	esv2758504	chr19:51991896-52266700	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	542 gene(s)	inside rSNPs	diseases
5	esv2758767	chr19:51991896-52604625	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	578 gene(s)	inside rSNPs	diseases
6	nsv469584	chr19:52001381-52151821	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv482654	chr19:52001381-52151821	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	esv33175	chr19:52002098-52010839	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs8110247	LAIR1	cis	cerebellum	SCAN
rs8110247	SIGLEC12	cis	Whole Blood	GTEx
rs8110247	NCR1	cis	parietal	SCAN
rs8110247	NAT14	cis	cerebellum	SCAN
rs8110247	SIGLEC5	cis	lymphoblastoid	seeQTL
rs8110247	NLRP4	cis	cerebellum	SCAN
rs8110247	ZNF274	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52002600-52015000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr19:52007000-52010800	Enhancers	Monocytes-CD14+_RO01746	blood
3	chr19:52007800-52011000	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr19:52008400-52010800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr19:52009400-52011800	Enhancers	Duodenum Mucosa	Duodenum
6	chr19:52009400-52011800	Enhancers	Fetal Intestine Large	intestine
7	chr19:52009400-52012000	Enhancers	Fetal Intestine Small	intestine
8	chr19:52009800-52012400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr19:52010400-52012200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr19:52010400-52012400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr19:52010400-52012600	Flanking Active TSS	K562	blood

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