Variant report

Variant	rs62248599
Chromosome Location	chr3:47516728-47516729
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47421161..47424382-chr3:47515710..47518539,3	MCF-7	breast:
2	chr3:47515959..47519018-chr3:47554813..47558530,7	K562	blood:
3	chr3:47421212..47424258-chr3:47516702..47519185,3	K562	blood:
4	chr3:47515849..47519127-chr3:47552237..47555413,3	MCF-7	breast:
5	chr3:47514858..47522453-chr3:47552535..47558710,16	K562	blood:
6	chr3:47513969..47516839-chr3:47829270..47830805,2	K562	blood:

Variant related genes	Relation type
ENSG00000076201	Chromatin interaction
ENSG00000163832	Chromatin interaction
ENSG00000260236	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1038394	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10865946	0.84[EUR][1000 genomes]
rs11130128	0.85[AFR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11130129	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11130132	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11130133	0.89[EUR][1000 genomes]
rs11130137	0.86[EUR][1000 genomes]
rs11705957	0.84[EUR][1000 genomes]
rs11707895	0.86[EUR][1000 genomes]
rs11711265	0.89[EUR][1000 genomes]
rs11711824	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11712445	0.84[EUR][1000 genomes]
rs11713413	0.83[EUR][1000 genomes]
rs11716763	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719877	0.84[EUR][1000 genomes]
rs11914913	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11914932	0.90[EUR][1000 genomes]
rs11925823	0.84[EUR][1000 genomes]
rs12486969	0.84[EUR][1000 genomes]
rs12487736	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12489046	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12490058	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12492433	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12497225	0.85[EUR][1000 genomes]
rs12630641	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12632132	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12636851	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13059519	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13064843	0.84[EUR][1000 genomes]
rs13075233	0.84[EUR][1000 genomes]
rs13079098	0.83[EUR][1000 genomes]
rs1531875	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17784882	0.91[EUR][1000 genomes]
rs1872164	0.85[EUR][1000 genomes]
rs2062278	0.85[EUR][1000 genomes]
rs2101247	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2291298	0.90[EUR][1000 genomes]
rs34634681	0.86[EUR][1000 genomes]
rs3736177	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3816779	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4599332	0.85[EUR][1000 genomes]
rs4858805	0.83[EUR][1000 genomes]
rs4858848	0.82[EUR][1000 genomes]
rs4858856	0.88[EUR][1000 genomes]
rs4858868	0.86[EUR][1000 genomes]
rs4858894	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56032309	0.85[EUR][1000 genomes]
rs56351005	0.83[EUR][1000 genomes]
rs57346147	0.85[EUR][1000 genomes]
rs59586735	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60369822	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62248603	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62248605	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62260710	0.88[EUR][1000 genomes]
rs62260711	0.88[EUR][1000 genomes]
rs62260741	0.83[EUR][1000 genomes]
rs6765990	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6787422	0.84[EUR][1000 genomes]
rs6790763	0.85[EUR][1000 genomes]
rs6792461	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6792488	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6800271	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73081205	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7628631	0.90[EUR][1000 genomes]
rs7641010	0.81[EUR][1000 genomes]
rs7649234	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7651194	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7651762	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs878659	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs922957	0.85[EUR][1000 genomes]
rs9683033	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9683177	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv3806	chr3:47488784-47518133	Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62248599	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs62248599	SETD2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47515200-47517800	Active TSS	GM12878-XiMat	blood
2	chr3:47515400-47518400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:47515600-47518000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:47515800-47517000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:47515800-47518000	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr3:47515800-47518000	Active TSS	Hela-S3	cervix
7	chr3:47516000-47516800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr3:47516000-47516800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr3:47516000-47516800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
10	chr3:47516000-47516800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
11	chr3:47516000-47516800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:47516000-47516800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr3:47516000-47516800	Flanking Active TSS	Brain Angular Gyrus	brain
14	chr3:47516000-47516800	Flanking Active TSS	Fetal Brain Female	brain
15	chr3:47516000-47516800	Flanking Active TSS	Stomach Smooth Muscle	stomach
16	chr3:47516000-47517000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:47516000-47517000	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr3:47516000-47517000	Active TSS	Right Atrium	heart
19	chr3:47516000-47517200	Flanking Active TSS	Primary hematopoietic stem cells	blood
20	chr3:47516000-47517600	Active TSS	H1 Cell Line	embryonic stem cell
21	chr3:47516000-47517600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:47516000-47517600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:47516000-47517800	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr3:47516000-47517800	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr3:47516000-47517800	Active TSS	HMEC	breast
26	chr3:47516000-47517800	Active TSS	NHEK	skin
27	chr3:47516000-47518000	Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr3:47516000-47518000	Active TSS	H9 Cell Line	embryonic stem cell
29	chr3:47516000-47518000	Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr3:47516000-47518000	Active TSS	HUES64 Cell Line	embryonic stem cell
31	chr3:47516000-47518000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:47516000-47518000	Active TSS	A549	lung
33	chr3:47516000-47518000	Active TSS	NHDF-Ad	bronchial
34	chr3:47516000-47518000	Active TSS	NHLF	lung
35	chr3:47516000-47518200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:47516000-47518200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:47516000-47518200	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr3:47516200-47516800	Flanking Active TSS	Primary T cells from cord blood	blood
39	chr3:47516200-47516800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
40	chr3:47516200-47516800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
41	chr3:47516200-47516800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
42	chr3:47516200-47516800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr3:47516200-47516800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
44	chr3:47516200-47516800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr3:47516200-47516800	Flanking Active TSS	Brain Germinal Matrix	brain
46	chr3:47516200-47516800	Flanking Active TSS	Brain Hippocampus Middle	brain
47	chr3:47516200-47516800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr3:47516200-47516800	Flanking Active TSS	Fetal Lung	lung
49	chr3:47516200-47516800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
50	chr3:47516200-47516800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

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