Variant report

Variant	rs1169720
Chromosome Location	chr12:121641034-121641035
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:121608796..121609410-chr12:121640363..121641099,2	MCF-7	breast:
2	chr12:121640765..121641418-chr12:121664955..121665790,2	MCF-7	breast:
3	chr12:121639319..121642998-chr12:121646427..121652052,9	MCF-7	breast:
4	chr12:121638895..121643738-chr12:121644037..121648634,7	K562	blood:
5	chr12:121633584..121637006-chr12:121640952..121642705,3	K562	blood:
6	chr12:121640762..121641344-chr12:121664895..121665592,2	MCF-7	breast:
7	chr12:121613491..121614418-chr12:121640538..121641644,9	MCF-7	breast:
8	chr12:121613587..121614418-chr12:121640538..121641398,7	MCF-7	breast:
9	chr12:121638895..121644396-chr12:121646510..121649736,6	K562	blood:
10	chr12:121638580..121643612-chr12:121646421..121651534,9	MCF-7	breast:
11	chr12:121569572..121570160-chr12:121640475..121641223,2	MCF-7	breast:
12	chr12:121634221..121637382-chr12:121639150..121642465,4	K562	blood:
13	chr12:121569636..121570366-chr12:121640682..121641273,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000135124	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10774587	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10774589	0.90[JPT][hapmap]
rs10849852	0.89[AFR][1000 genomes]
rs10849855	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10849856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10849858	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11065479	0.92[AMR][1000 genomes]
rs11065486	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1169727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1180051	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1182945	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1629287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1653622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1653623	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1718117	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2071271	0.83[ASN][1000 genomes]
rs2393849	0.86[ASN][1000 genomes]
rs2393850	0.84[ASN][1000 genomes]
rs25643	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2567978	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2567980	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2567993	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2567994	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2668235	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2668252	0.96[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2686362	0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs2686363	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2686387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2686388	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2942063	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58232824	0.86[ASN][1000 genomes]
rs6489799	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs725135	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7298368	0.85[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs930186	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs930187	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv560454	chr12:121457073-121745742	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1054878	chr12:121519880-121761800	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv455729	chr12:121525591-121761800	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv560455	chr12:121525591-121761800	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv1050519	chr12:121552964-121756420	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer 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	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1169720	P2RX4	cis	multi-tissue	Pritchard

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121624200-121647200	Weak transcription	Brain Anterior Caudate	brain
2	chr12:121625600-121647200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr12:121628000-121647200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:121630400-121647200	Weak transcription	Brain Hippocampus Middle	brain
5	chr12:121637200-121642800	Weak transcription	HUVEC	blood vessel
6	chr12:121639600-121641600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:121639800-121641400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr12:121640400-121641200	Enhancers	HepG2	liver
9	chr12:121640400-121641400	Enhancers	Fetal Heart	heart
10	chr12:121640400-121641600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:121640400-121641600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr12:121640600-121641200	Enhancers	Primary hematopoietic stem cells	blood
13	chr12:121640600-121641200	Enhancers	Fetal Lung	lung
14	chr12:121640600-121641400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr12:121640600-121641400	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr12:121640800-121641200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr12:121640800-121641400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:121640800-121641400	Enhancers	Placenta	Placenta
19	chr12:121641000-121641600	Enhancers	K562	blood
20	chr12:121641000-121647000	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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