Variant report

Variant	rs59586735
Chromosome Location	chr3:47518325-47518326
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MTA3	chr3:47517334-47518363	GM12878	blood:	n/a	n/a
2	NRF1	chr3:47516469-47518325	SK-N-SH	brain:	n/a	chr3:47517482-47517493 chr3:47517502-47517513 chr3:47517499-47517513 chr3:47517502-47517516 chr3:47517502-47517511 chr3:47517501-47517512
3	SREBP1	chr3:47516551-47518383	GM12878	blood:	n/a	n/a
4	HCFC1	chr3:47516150-47518513	Hela-S3	cervix:	n/a	n/a
5	MXI1	chr3:47516110-47518326	IMR90	lung:	n/a	chr3:47518263-47518272

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	chr3:47516853..47519140-chr3:47552540..47554804,2	K562	blood:
4	chr3:47517000..47518898-chr3:47553503..47555286,3	MCF-7	breast:
5	chr3:47421212..47424258-chr3:47516702..47519185,3	K562	blood:
6	chr3:47515849..47519127-chr3:47552237..47555413,3	MCF-7	breast:
7	chr3:47514858..47522453-chr3:47552535..47558710,16	K562	blood:

Variant related genes	Relation type
SCAP	TF binding region
ENSG00000260236	Chromatin interaction
ENSG00000163832	Chromatin interaction
ENSG00000076201	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1038394	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10865946	0.85[EUR][1000 genomes]
rs11130128	0.86[AFR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11130129	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11130132	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11130133	0.91[EUR][1000 genomes]
rs11130137	0.87[EUR][1000 genomes]
rs11705957	0.86[EUR][1000 genomes]
rs11707895	0.88[EUR][1000 genomes]
rs11711265	0.91[EUR][1000 genomes]
rs11711824	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11712445	0.86[EUR][1000 genomes]
rs11713413	0.85[EUR][1000 genomes]
rs11716763	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719877	0.86[EUR][1000 genomes]
rs11914913	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11914932	0.91[EUR][1000 genomes]
rs11925823	0.85[EUR][1000 genomes]
rs12486969	0.85[EUR][1000 genomes]
rs12487736	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12489046	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12490058	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12492433	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12497225	0.86[EUR][1000 genomes]
rs12630641	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12632132	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12636851	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13059519	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13064843	0.86[EUR][1000 genomes]
rs13075233	0.86[EUR][1000 genomes]
rs13079098	0.84[EUR][1000 genomes]
rs1531875	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17784882	0.93[EUR][1000 genomes]
rs1872164	0.86[EUR][1000 genomes]
rs2062278	0.86[EUR][1000 genomes]
rs2101247	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2291298	0.91[EUR][1000 genomes]
rs34634681	0.87[EUR][1000 genomes]
rs3736177	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3816779	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4599332	0.87[EUR][1000 genomes]
rs4858805	0.85[EUR][1000 genomes]
rs4858848	0.84[EUR][1000 genomes]
rs4858856	0.89[EUR][1000 genomes]
rs4858868	0.88[EUR][1000 genomes]
rs4858894	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56032309	0.86[EUR][1000 genomes]
rs56351005	0.85[EUR][1000 genomes]
rs57346147	0.86[EUR][1000 genomes]
rs60369822	0.84[AFR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62248599	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62248603	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62248605	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62260710	0.90[EUR][1000 genomes]
rs62260711	0.90[EUR][1000 genomes]
rs62260741	0.85[EUR][1000 genomes]
rs6765990	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6787422	0.86[EUR][1000 genomes]
rs6790763	0.86[EUR][1000 genomes]
rs6792461	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6792488	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6800271	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73081205	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7628631	0.91[EUR][1000 genomes]
rs7641010	0.82[EUR][1000 genomes]
rs7649234	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7651194	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7651762	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs878659	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs922957	0.86[EUR][1000 genomes]
rs9683033	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9683177	0.97[EUR][1000 genomes];0.93[ASN][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
rs59586735	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs59586735	KLHL18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47515400-47518400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr3:47516600-47518400	Active TSS	HSMM	muscle
3	chr3:47516800-47518400	Active TSS	Fetal Brain Female	brain
4	chr3:47516800-47518400	Active TSS	Thymus	Thymus
5	chr3:47517400-47518600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:47517400-47523000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:47517600-47518400	Flanking Active TSS	Primary T cells from cord blood	blood
8	chr3:47517600-47518400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr3:47517600-47518400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
10	chr3:47517600-47518400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
11	chr3:47517600-47518400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:47517600-47518400	Flanking Active TSS	Colonic Mucosa	Colon
13	chr3:47517600-47518400	Flanking Active TSS	Fetal Muscle Leg	muscle
14	chr3:47517600-47518600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
15	chr3:47517600-47518600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:47517600-47518600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr3:47517600-47518600	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr3:47517600-47518600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr3:47517600-47518800	Flanking Active TSS	Stomach Smooth Muscle	stomach
20	chr3:47517600-47523000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr3:47517800-47518400	Enhancers	H1 Cell Line	embryonic stem cell
22	chr3:47517800-47518400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:47517800-47518400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
24	chr3:47517800-47518400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:47517800-47518400	Flanking Active TSS	Brain Substantia Nigra	brain
26	chr3:47517800-47518400	Flanking Active TSS	Rectal Smooth Muscle	rectum
27	chr3:47517800-47518400	Flanking Active TSS	GM12878-XiMat	blood
28	chr3:47517800-47518400	Flanking Active TSS	HepG2	liver
29	chr3:47517800-47518400	Flanking Active TSS	NHEK	skin
30	chr3:47517800-47518600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
31	chr3:47517800-47518600	Flanking Active TSS	Brain Angular Gyrus	brain
32	chr3:47517800-47518600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr3:47517800-47518600	Enhancers	Placenta Amnion	Placenta Amnion
34	chr3:47517800-47518600	Flanking Active TSS	K562	blood
35	chr3:47517800-47518800	Enhancers	Spleen	Spleen
36	chr3:47517800-47518800	Flanking Active TSS	Dnd41	blood
37	chr3:47517800-47520600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr3:47517800-47523000	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr3:47517800-47527200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr3:47517800-47535200	Weak transcription	Esophagus	oesophagus
41	chr3:47517800-47536600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:47517800-47544400	Weak transcription	Small Intestine	intestine
43	chr3:47518000-47518400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:47518000-47518400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:47518000-47518400	Enhancers	Primary hematopoietic stem cells	blood
46	chr3:47518000-47518400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr3:47518000-47518400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr3:47518000-47518400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr3:47518000-47518400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr3:47518000-47518400	Enhancers	Aorta	Aorta

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