Variant report

Variant	rs1814565
Chromosome Location	chr3:142716921-142716922
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	SPI1	chr3:142716912-142717149	K562	blood:	n/a	n/a
2	POLR2A	chr3:142716794-142717067	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:142651551..142654466-chr3:142715710..142718013,2	K562	blood:
2	chr3:142716811..142718483-chr3:142789179..142792100,2	K562	blood:
3	chr3:142705633..142707723-chr3:142715546..142717712,2	MCF-7	breast:
4	chr3:142639165..142641900-chr3:142716819..142719641,2	K562	blood:

Variant related genes	Relation type
U2SURP	TF binding region

Extended variants
information (count: 90 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10413	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1043898	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs10451867	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10513184	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1053950	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs10790	0.85[CEU][hapmap];0.86[CHB][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs10935474	0.82[EUR][1000 genomes]
rs10935475	0.96[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10935479	0.89[EUR][1000 genomes]
rs11709036	1.00[CEU][hapmap];0.85[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.80[TSI][hapmap]
rs11915462	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11922201	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12485790	0.89[EUR][1000 genomes]
rs12490776	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12492904	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12695770	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13075955	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13094293	0.96[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs13099995	0.85[EUR][1000 genomes]
rs1349262	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[EUR][1000 genomes]
rs13715	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1375814	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1449868	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs1449869	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs1530753	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[EUR][1000 genomes]
rs1532588	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[EUR][1000 genomes]
rs1545597	0.90[EUR][1000 genomes]
rs17557029	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1827159	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[EUR][1000 genomes]
rs1839406	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[EUR][1000 genomes]
rs1868569	0.88[EUR][1000 genomes]
rs1868570	0.88[EUR][1000 genomes]
rs1965343	0.96[CEU][hapmap];0.86[CHB][hapmap];0.94[EUR][1000 genomes]
rs2045306	0.90[EUR][1000 genomes]
rs2124541	0.96[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs2124542	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2124543	0.96[CEU][hapmap];0.80[CHB][hapmap];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2137586	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2175739	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2290549	0.85[CEU][hapmap];0.86[CHB][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs2353408	0.87[EUR][1000 genomes]
rs2353409	0.90[EUR][1000 genomes]
rs2353411	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs3821645	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[EUR][1000 genomes]
rs3856697	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs3902877	0.96[CEU][hapmap];0.90[CHB][hapmap];0.96[EUR][1000 genomes]
rs4030582	0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[EUR][1000 genomes]
rs4683444	0.89[EUR][1000 genomes]
rs4683721	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4683722	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs4683723	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4683724	0.87[EUR][1000 genomes]
rs56382522	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6440129	0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[EUR][1000 genomes]
rs6440131	0.89[EUR][1000 genomes]
rs6440132	0.87[EUR][1000 genomes]
rs6440133	0.82[EUR][1000 genomes]
rs6440134	0.96[CEU][hapmap];0.85[CHB][hapmap];0.90[EUR][1000 genomes]
rs6770102	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6778454	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6781080	0.93[EUR][1000 genomes]
rs6781887	0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[EUR][1000 genomes]
rs6783145	0.87[EUR][1000 genomes]
rs6784200	0.96[CEU][hapmap];0.91[GIH][hapmap]
rs6796771	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs6802376	0.85[EUR][1000 genomes]
rs6805417	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs6806551	0.88[EUR][1000 genomes]
rs6808689	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[EUR][1000 genomes]
rs7611721	0.96[CEU][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs7623532	0.89[EUR][1000 genomes]
rs7644475	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7648143	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs7649225	0.84[EUR][1000 genomes]
rs7652745	0.85[CEU][hapmap];0.86[CHB][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs766360	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs936194	0.90[EUR][1000 genomes]
rs936196	0.88[EUR][1000 genomes]
rs936197	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs937498	0.96[CEU][hapmap];0.90[CHB][hapmap];0.88[EUR][1000 genomes]
rs9814656	0.92[CEU][hapmap];0.86[CHB][hapmap];0.89[EUR][1000 genomes]
rs9816317	0.90[EUR][1000 genomes]
rs9835348	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9847059	0.88[EUR][1000 genomes]
rs9851353	0.88[EUR][1000 genomes]
rs9862433	0.88[EUR][1000 genomes]
rs9877128	0.89[EUR][1000 genomes]
rs9877135	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877562	chr3:142573789-142846370	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv877563	chr3:142661350-142743889	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1814565	U2SURP	cis	lymphoblastoid	seeQTL
rs1814565	CHST2	cis	parietal	SCAN
rs1814565	SR140	Cis_1M	lymphoblastoid	RTeQTL
rs1814565	SR140	cis	multi-tissue	Pritchard
rs1814565	SLC9A9	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142707000-142718800	Weak transcription	Right Ventricle	heart
2	chr3:142710200-142718600	Weak transcription	GM12878-XiMat	blood
3	chr3:142711000-142718400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:142713000-142718600	Weak transcription	A549	lung
5	chr3:142715400-142718000	Enhancers	HepG2	liver
6	chr3:142716000-142717800	Flanking Active TSS	Hela-S3	cervix
7	chr3:142716200-142717000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:142716200-142717200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr3:142716200-142717800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:142716200-142718600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:142716400-142717000	Enhancers	Fetal Kidney	kidney
12	chr3:142716400-142717600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:142716400-142717600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr3:142716400-142717600	Enhancers	NHDF-Ad	bronchial
15	chr3:142716400-142717600	Enhancers	NHEK	skin
16	chr3:142716400-142717600	Enhancers	Osteobl	bone
17	chr3:142716400-142719400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:142716600-142718400	Weak transcription	Adipose Nuclei	Adipose
19	chr3:142716600-142718600	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr3:142716600-142718600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:142716600-142718600	Weak transcription	Fetal Lung	lung
22	chr3:142716600-142719000	Weak transcription	HSMM	muscle
23	chr3:142716800-142718000	Enhancers	K562	blood
24	chr3:142716800-142718400	Weak transcription	HMEC	breast
25	chr3:142716800-142719000	Enhancers	NHLF	lung

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