Variant report

Variant	rs56032309
Chromosome Location	chr3:47431417-47431418
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47420219..47422080-chr3:47430722..47433215,2	K562	blood:

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

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

rs_ID	r²[population]
rs1038394	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10865946	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11130127	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11130128	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11130129	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11130132	0.83[EUR][1000 genomes]
rs11130133	0.81[EUR][1000 genomes]
rs11705957	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11711265	0.81[EUR][1000 genomes]
rs11711824	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11712445	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11716763	0.86[EUR][1000 genomes]
rs11719877	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11914913	0.81[EUR][1000 genomes]
rs11914932	0.81[EUR][1000 genomes]
rs11925823	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11927371	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12486969	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12487736	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12489046	0.86[EUR][1000 genomes]
rs12490058	0.83[EUR][1000 genomes]
rs12492433	0.86[EUR][1000 genomes]
rs12497225	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12630641	0.81[EUR][1000 genomes]
rs12632132	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12636851	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13059519	0.82[EUR][1000 genomes]
rs13064843	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13075233	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13079098	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1531875	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17411375	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17784882	0.83[EUR][1000 genomes]
rs1872164	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2062278	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2101247	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2159400	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2291298	0.81[EUR][1000 genomes]
rs295428	0.86[EUR][1000 genomes]
rs295449	0.87[EUR][1000 genomes]
rs295458	0.87[EUR][1000 genomes]
rs295461	0.86[EUR][1000 genomes]
rs3736177	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3816779	0.81[EUR][1000 genomes]
rs4241548	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4858805	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4858848	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4858868	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4858888	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4858890	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4858894	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs553989	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56351005	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57346147	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59586735	0.86[EUR][1000 genomes]
rs60369822	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62246474	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62248580	0.89[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs62248599	0.85[EUR][1000 genomes]
rs6765990	0.82[EUR][1000 genomes]
rs6780013	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6787422	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6792461	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6792488	0.87[EUR][1000 genomes]
rs6800271	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73081205	0.84[EUR][1000 genomes]
rs7613282	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7628631	0.81[EUR][1000 genomes]
rs7641010	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7649234	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7651194	0.82[EUR][1000 genomes]
rs7651762	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs807810	0.89[EUR][1000 genomes]
rs807931	0.87[EUR][1000 genomes]
rs8180040	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs878659	0.88[EUR][1000 genomes]
rs922957	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9683033	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9683177	0.87[EUR][1000 genomes];0.84[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
rs56032309	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs56032309	KLHL18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47423600-47431800	Weak transcription	Lung	lung
2	chr3:47423600-47435400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:47423600-47435400	Weak transcription	Aorta	Aorta
4	chr3:47423600-47446000	Weak transcription	Colonic Mucosa	Colon
5	chr3:47423800-47433800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:47423800-47435000	Weak transcription	Fetal Heart	heart
7	chr3:47423800-47435000	Weak transcription	NHDF-Ad	bronchial
8	chr3:47423800-47435400	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr3:47423800-47435400	Weak transcription	Fetal Lung	lung
10	chr3:47423800-47435400	Weak transcription	NH-A	brain
11	chr3:47423800-47435600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr3:47423800-47435600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr3:47423800-47435600	Weak transcription	Hela-S3	cervix
14	chr3:47423800-47435600	Weak transcription	HSMMtube	muscle
15	chr3:47423800-47435800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:47423800-47436400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr3:47423800-47436600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr3:47423800-47438800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr3:47423800-47447400	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr3:47423800-47448000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr3:47423800-47449800	Weak transcription	A549	lung
22	chr3:47424000-47436400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr3:47424000-47446000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr3:47424600-47433200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr3:47424800-47435600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr3:47425200-47432400	Strong transcription	Fetal Stomach	stomach
27	chr3:47425200-47435600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr3:47425400-47433200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:47425400-47434200	Strong transcription	Fetal Muscle Leg	muscle
30	chr3:47425400-47435600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr3:47425400-47435600	Weak transcription	Adipose Nuclei	Adipose
32	chr3:47425400-47435600	Weak transcription	Small Intestine	intestine
33	chr3:47425400-47435800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr3:47425600-47435600	Weak transcription	Brain Anterior Caudate	brain
35	chr3:47426200-47462400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr3:47426600-47432200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:47427000-47435600	Weak transcription	HMEC	breast
38	chr3:47427200-47435400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:47427200-47435600	Weak transcription	Stomach Mucosa	stomach
40	chr3:47427400-47435200	Strong transcription	Fetal Intestine Small	intestine
41	chr3:47427400-47435400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr3:47427400-47435800	Weak transcription	Esophagus	oesophagus
43	chr3:47427600-47431600	Weak transcription	Ovary	ovary
44	chr3:47427600-47433400	Weak transcription	Fetal Brain Female	brain
45	chr3:47427600-47435400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr3:47427600-47435600	Weak transcription	Brain Substantia Nigra	brain
47	chr3:47427600-47435600	Weak transcription	Right Ventricle	heart
48	chr3:47427600-47436600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr3:47427600-47448400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr3:47427800-47433800	Weak transcription	Pancreas	Pancrea

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