Variant report

Variant	rs56351005
Chromosome Location	chr3:47430186-47430187
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47121965..47124709-chr3:47429013..47430772,2	K562	blood:
2	chr3:47324292..47325959-chr3:47428265..47430683,2	K562	blood:
3	chr3:47428453..47430945-chr3:47431745..47434301,2	K562	blood:

Variant related genes	Relation type
ENSG00000088727	Chromatin interaction
ENSG00000114648	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

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

Chromatin state (count:120 , 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	chr3:47423800-47430200	Weak transcription	HUVEC	blood vessel
6	chr3:47423800-47430400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:47423800-47433800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr3:47423800-47435000	Weak transcription	Fetal Heart	heart
9	chr3:47423800-47435000	Weak transcription	NHDF-Ad	bronchial
10	chr3:47423800-47435400	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr3:47423800-47435400	Weak transcription	Fetal Lung	lung
12	chr3:47423800-47435400	Weak transcription	NH-A	brain
13	chr3:47423800-47435600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr3:47423800-47435600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:47423800-47435600	Weak transcription	Hela-S3	cervix
16	chr3:47423800-47435600	Weak transcription	HSMMtube	muscle
17	chr3:47423800-47435800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:47423800-47436400	Weak transcription	Primary hematopoietic stem cells	blood
19	chr3:47423800-47436600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr3:47423800-47438800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr3:47423800-47447400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr3:47423800-47448000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr3:47423800-47449800	Weak transcription	A549	lung
24	chr3:47424000-47436400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr3:47424000-47446000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr3:47424600-47431000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:47424600-47431000	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr3:47424600-47433200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr3:47424800-47430200	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr3:47424800-47430400	Weak transcription	Spleen	Spleen
31	chr3:47424800-47435600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr3:47425000-47430600	Weak transcription	Fetal Kidney	kidney
33	chr3:47425000-47431000	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr3:47425200-47432400	Strong transcription	Fetal Stomach	stomach
35	chr3:47425200-47435600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr3:47425400-47430400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr3:47425400-47430800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr3:47425400-47433200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:47425400-47434200	Strong transcription	Fetal Muscle Leg	muscle
40	chr3:47425400-47435600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr3:47425400-47435600	Weak transcription	Adipose Nuclei	Adipose
42	chr3:47425400-47435600	Weak transcription	Small Intestine	intestine
43	chr3:47425400-47435800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr3:47425600-47435600	Weak transcription	Brain Anterior Caudate	brain
45	chr3:47426200-47430800	Strong transcription	Primary T cells from cord blood	blood
46	chr3:47426200-47462400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr3:47426600-47430800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:47426600-47430800	Strong transcription	Osteobl	bone
49	chr3:47426600-47431000	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr3:47426600-47432200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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