Variant report

Variant	rs11130133
Chromosome Location	chr3:47547664-47547665
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:47544325..47548888-chr3:47549831..47552841,6	K562	blood:

Variant related genes	Relation type
ENSG00000163832	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1038394	0.82[EUR][1000 genomes]
rs11130128	0.88[EUR][1000 genomes]
rs11130129	0.88[EUR][1000 genomes]
rs11130132	0.96[EUR][1000 genomes]
rs11130137	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11705957	0.80[EUR][1000 genomes]
rs11707895	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11711265	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11711824	0.81[EUR][1000 genomes]
rs11712445	0.80[EUR][1000 genomes]
rs11713413	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11716763	0.91[EUR][1000 genomes]
rs11719877	0.80[EUR][1000 genomes]
rs11914795	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11914913	0.84[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs11914932	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12489046	0.90[EUR][1000 genomes]
rs12490058	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12492433	0.90[EUR][1000 genomes]
rs12497225	0.81[EUR][1000 genomes]
rs12630641	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12632132	0.81[EUR][1000 genomes]
rs12636851	0.82[EUR][1000 genomes]
rs13059519	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13064843	0.80[EUR][1000 genomes]
rs13075233	0.80[EUR][1000 genomes]
rs1531875	0.81[EUR][1000 genomes]
rs1564760	0.87[ASN][1000 genomes]
rs1564761	0.90[ASN][1000 genomes]
rs17784882	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1872164	0.81[EUR][1000 genomes]
rs1872166	0.90[ASN][1000 genomes]
rs2062278	0.81[EUR][1000 genomes]
rs2101247	0.88[EUR][1000 genomes]
rs2291298	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34634681	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3736177	0.81[EUR][1000 genomes]
rs3816779	0.82[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs4599332	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4858856	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4858868	0.81[EUR][1000 genomes]
rs4858894	0.86[EUR][1000 genomes]
rs56032309	0.81[EUR][1000 genomes]
rs57346147	0.81[EUR][1000 genomes]
rs59586735	0.91[EUR][1000 genomes]
rs60369822	0.86[EUR][1000 genomes]
rs62248599	0.89[EUR][1000 genomes]
rs62248603	0.85[EUR][1000 genomes]
rs62248605	0.91[EUR][1000 genomes]
rs62260710	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62260711	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62260741	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6765990	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6768879	0.85[ASN][1000 genomes]
rs6787422	0.80[EUR][1000 genomes]
rs6790763	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6792461	0.81[EUR][1000 genomes]
rs6792488	0.87[EUR][1000 genomes]
rs6800271	0.81[EUR][1000 genomes]
rs73081205	0.89[EUR][1000 genomes]
rs7628631	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7649234	0.88[EUR][1000 genomes]
rs7651194	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7651762	0.81[EUR][1000 genomes]
rs878659	0.88[EUR][1000 genomes]
rs922957	0.81[EUR][1000 genomes]
rs9683033	0.88[EUR][1000 genomes]
rs9683177	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11130133	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs11130133	KLHL18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47534600-47553000	Strong transcription	Fetal Thymus	thymus
2	chr3:47534800-47549400	Weak transcription	Fetal Heart	heart
3	chr3:47534800-47552400	Strong transcription	Fetal Intestine Small	intestine
4	chr3:47534800-47553200	Strong transcription	Fetal Stomach	stomach
5	chr3:47535200-47553000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:47535600-47552800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:47536200-47553200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:47536600-47553000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:47537200-47553800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:47538400-47554000	Weak transcription	Stomach Mucosa	stomach
11	chr3:47539000-47553800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr3:47540400-47550800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr3:47541400-47554000	Weak transcription	Right Atrium	heart
14	chr3:47543200-47550800	Weak transcription	Fetal Kidney	kidney
15	chr3:47543600-47551400	Weak transcription	NHDF-Ad	bronchial
16	chr3:47543600-47553000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr3:47544800-47553400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr3:47544800-47553800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr3:47545000-47552800	Weak transcription	Fetal Brain Male	brain
20	chr3:47545600-47551000	Weak transcription	Primary hematopoietic stem cells	blood
21	chr3:47545600-47553400	Weak transcription	A549	lung
22	chr3:47545800-47549000	Weak transcription	Primary B cells from cord blood	blood
23	chr3:47545800-47549200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:47545800-47554000	Weak transcription	Colon Smooth Muscle	Colon
25	chr3:47546000-47548200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr3:47546000-47548200	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr3:47546000-47548400	Weak transcription	Fetal Intestine Large	intestine
28	chr3:47546000-47548400	Weak transcription	Pancreas	Pancrea
29	chr3:47546000-47548600	Weak transcription	Brain Substantia Nigra	brain
30	chr3:47546000-47548800	Weak transcription	GM12878-XiMat	blood
31	chr3:47546000-47549000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr3:47546000-47549200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:47546000-47549200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr3:47546000-47549200	Weak transcription	Ovary	ovary
35	chr3:47546000-47549200	Weak transcription	Osteobl	bone
36	chr3:47546000-47549400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr3:47546000-47549400	Weak transcription	NHLF	lung
38	chr3:47546000-47550000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:47546000-47550600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr3:47546000-47550600	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr3:47546000-47550600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr3:47546000-47550600	Weak transcription	Colonic Mucosa	Colon
43	chr3:47546000-47550800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr3:47546000-47550800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr3:47546000-47550800	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr3:47546000-47550800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr3:47546000-47550800	Weak transcription	Fetal Lung	lung
48	chr3:47546000-47550800	Weak transcription	Left Ventricle	heart
49	chr3:47546000-47550800	Weak transcription	Hela-S3	cervix
50	chr3:47546000-47550800	Weak transcription	HMEC	breast

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