Variant report

Variant	rs12497225
Chromosome Location	chr3:47426346-47426347
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47425391..47427606-chr3:47448113..47450358,2	K562	blood:
2	chr3:47422470..47424996-chr3:47425920..47429233,6	K562	blood:

Variant related genes	Relation type
ENSG00000260236	Chromatin interaction
ENSG00000076201	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	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10865946	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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];0.82[ASN][1000 genomes]
rs11130129	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11130132	0.83[EUR][1000 genomes]
rs11130133	0.81[EUR][1000 genomes]
rs11705957	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11711265	0.81[EUR][1000 genomes]
rs11711824	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11712445	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11716763	0.86[EUR][1000 genomes]
rs11719877	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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];0.92[ASN][1000 genomes]
rs11927371	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12486969	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12487736	0.90[EUR][1000 genomes]
rs12489046	0.86[EUR][1000 genomes]
rs12490058	0.83[EUR][1000 genomes]
rs12492433	0.86[EUR][1000 genomes]
rs12630641	0.81[EUR][1000 genomes]
rs12632132	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12636851	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[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];0.97[ASN][1000 genomes]
rs13079098	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1531875	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17411375	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17784882	0.83[EUR][1000 genomes]
rs1872164	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2062278	0.95[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];0.81[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	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3816779	0.81[EUR][1000 genomes]
rs4241548	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4858805	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4858848	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4858868	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[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];0.81[ASN][1000 genomes]
rs553989	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56032309	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56351005	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57346147	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59586735	0.86[EUR][1000 genomes]
rs60369822	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62246474	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62248580	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs62248599	0.85[EUR][1000 genomes]
rs6765990	0.82[EUR][1000 genomes]
rs6780013	0.81[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	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6792488	0.87[EUR][1000 genomes]
rs6800271	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[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	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7649234	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7651194	0.82[EUR][1000 genomes]
rs7651762	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[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	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9683033	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9683177	0.87[EUR][1000 genomes];0.82[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
rs12497225	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs12497225	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	chr3:47423600-47426400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:47423600-47427000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:47423600-47427000	Weak transcription	Esophagus	oesophagus
4	chr3:47423600-47427200	Weak transcription	Right Ventricle	heart
5	chr3:47423600-47429400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:47423600-47431800	Weak transcription	Lung	lung
7	chr3:47423600-47435400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:47423600-47435400	Weak transcription	Aorta	Aorta
9	chr3:47423600-47446000	Weak transcription	Colonic Mucosa	Colon
10	chr3:47423800-47426600	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr3:47423800-47426600	Weak transcription	Osteobl	bone
12	chr3:47423800-47426800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:47423800-47426800	Weak transcription	Stomach Mucosa	stomach
14	chr3:47423800-47426800	Weak transcription	Thymus	Thymus
15	chr3:47423800-47427000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:47423800-47427200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:47423800-47427400	Weak transcription	HSMM	muscle
18	chr3:47423800-47429400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr3:47423800-47429800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr3:47423800-47429800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:47423800-47429800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr3:47423800-47430200	Weak transcription	HUVEC	blood vessel
23	chr3:47423800-47430400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr3:47423800-47433800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:47423800-47435000	Weak transcription	Fetal Heart	heart
26	chr3:47423800-47435000	Weak transcription	NHDF-Ad	bronchial
27	chr3:47423800-47435400	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr3:47423800-47435400	Weak transcription	Fetal Lung	lung
29	chr3:47423800-47435400	Weak transcription	NH-A	brain
30	chr3:47423800-47435600	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr3:47423800-47435600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr3:47423800-47435600	Weak transcription	Hela-S3	cervix
33	chr3:47423800-47435600	Weak transcription	HSMMtube	muscle
34	chr3:47423800-47435800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:47423800-47436400	Weak transcription	Primary hematopoietic stem cells	blood
36	chr3:47423800-47436600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr3:47423800-47438800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr3:47423800-47447400	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr3:47423800-47448000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr3:47423800-47449800	Weak transcription	A549	lung
41	chr3:47424000-47426600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr3:47424000-47426600	Weak transcription	Fetal Thymus	thymus
43	chr3:47424000-47429200	Weak transcription	Primary B cells from peripheral blood	blood
44	chr3:47424000-47436400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr3:47424000-47446000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr3:47424200-47429800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:47424400-47427400	Genic enhancers	Fetal Intestine Small	intestine
48	chr3:47424600-47426800	Weak transcription	Brain Hippocampus Middle	brain
49	chr3:47424600-47427200	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr3:47424600-47427200	Weak transcription	Primary B cells from cord blood	blood

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