Variant report

Variant	rs6787422
Chromosome Location	chr3:47418509-47418510
allele	G/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	POLR2A	chr3:47417646-47419968	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:47418351-47419243	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr3:47417906-47419271	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr3:47418448-47419043	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr3:47417903-47419071	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr3:47417923-47419142	K562	blood:	n/a	n/a
7	POLR2A	chr3:47418017-47418662	HepG2	liver:	n/a	n/a
8	POLR2A	chr3:47418384-47418689	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:47417993..47420029-chr3:47421038..47423395,2	MCF-7	breast:
2	chr3:47411140..47414912-chr3:47416429..47418901,3	K562	blood:
3	chr3:47412852..47414876-chr3:47416548..47419778,4	K562	blood:
4	chr3:47023369..47025258-chr3:47417930..47420658,2	MCF-7	breast:

Variant related genes	Relation type
PTPN23	TF binding region
ENSG00000160799	Chromatin interaction
ENSG00000076201	Chromatin interaction
ENSG00000260236	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1038394	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10865946	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11130127	0.88[EUR][1000 genomes]
rs11130128	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11130129	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11130132	0.83[EUR][1000 genomes]
rs11130133	0.80[EUR][1000 genomes]
rs11705957	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11711265	0.80[EUR][1000 genomes]
rs11711824	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11712445	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11716763	0.86[EUR][1000 genomes]
rs11719877	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11914913	0.80[EUR][1000 genomes]
rs11914932	0.81[EUR][1000 genomes]
rs11925823	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11927371	0.85[EUR][1000 genomes]
rs12486969	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12487736	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12489046	0.86[EUR][1000 genomes]
rs12490058	0.82[EUR][1000 genomes]
rs12492433	0.86[EUR][1000 genomes]
rs12497225	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12630641	0.81[EUR][1000 genomes]
rs12632132	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12636851	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13059519	0.82[EUR][1000 genomes]
rs13064843	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13075233	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13079098	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1531875	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17411375	0.88[EUR][1000 genomes]
rs17784882	0.82[EUR][1000 genomes]
rs1872164	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2062278	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2101247	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2159400	0.87[EUR][1000 genomes]
rs2291298	0.81[EUR][1000 genomes]
rs295428	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs295449	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs295458	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs295461	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3736177	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3816779	0.81[EUR][1000 genomes]
rs4241548	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4858805	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4858848	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4858868	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4858888	0.89[EUR][1000 genomes]
rs4858890	0.83[EUR][1000 genomes]
rs4858894	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs553989	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56032309	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56351005	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57346147	0.99[EUR][1000 genomes]
rs59586735	0.86[EUR][1000 genomes]
rs60369822	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62246474	0.88[EUR][1000 genomes]
rs62248580	0.90[EUR][1000 genomes]
rs62248599	0.84[EUR][1000 genomes]
rs6765990	0.82[EUR][1000 genomes]
rs6780013	0.89[EUR][1000 genomes]
rs6792461	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6792488	0.86[EUR][1000 genomes]
rs6800271	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73081205	0.84[EUR][1000 genomes]
rs7613282	0.87[EUR][1000 genomes]
rs7628631	0.81[EUR][1000 genomes]
rs7641010	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7649234	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7651194	0.82[EUR][1000 genomes]
rs7651762	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs807810	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs807931	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8180040	0.86[EUR][1000 genomes]
rs878659	0.88[EUR][1000 genomes]
rs922957	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9683033	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9683177	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	esv1807553	chr3:47393616-47470763	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv3802	chr3:47396674-47441951	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6787422	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs6787422	SETD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47401600-47421200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:47413200-47418600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr3:47413200-47418800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:47413200-47418800	Weak transcription	Liver	Liver
5	chr3:47413200-47420200	Weak transcription	Spleen	Spleen
6	chr3:47413200-47420400	Weak transcription	Fetal Intestine Large	intestine
7	chr3:47413200-47420600	Weak transcription	Adipose Nuclei	Adipose
8	chr3:47413400-47420400	Weak transcription	Fetal Intestine Small	intestine
9	chr3:47413400-47420800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:47413600-47421000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:47414200-47421000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr3:47416200-47420800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:47417000-47418600	Weak transcription	Placenta	Placenta
14	chr3:47417200-47420200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:47417600-47420600	Weak transcription	Brain Hippocampus Middle	brain
16	chr3:47417600-47421000	Weak transcription	NHLF	lung
17	chr3:47417800-47420400	Enhancers	HepG2	liver
18	chr3:47418000-47419800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr3:47418000-47420600	Enhancers	K562	blood
20	chr3:47418000-47421600	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr3:47418200-47418600	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr3:47418200-47418600	Enhancers	Brain Anterior Caudate	brain
23	chr3:47418200-47418600	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr3:47418200-47419000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:47418200-47419200	Enhancers	Pancreas	Pancrea
26	chr3:47418200-47419800	Strong transcription	Fetal Stomach	stomach
27	chr3:47418400-47419200	Enhancers	Primary B cells from cord blood	blood
28	chr3:47418400-47419200	Enhancers	Primary B cells from peripheral blood	blood
29	chr3:47418400-47419200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr3:47418400-47419400	Enhancers	Primary hematopoietic stem cells short term culture	blood

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