Variant report

Variant	rs2254494
Chromosome Location	chr1:220162195-220162196
allele	A/G
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	POLR2A	chr1:220161313-220168073	K562	blood:	n/a	n/a
2	ATF2	chr1:220161520-220162244	GM12878	blood:	n/a	n/a
3	BCLAF1	chr1:220161550-220162282	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:220153591..220159773-chr1:220159981..220165102,9	K562	blood:
2	chr1:220161264..220163445-chr1:220234115..220237098,2	K562	blood:

Variant related genes	Relation type
ENSG00000238798	TF binding region
EPRS	TF binding region
ENSG00000136628	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1061160	0.82[LWK][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes]
rs12140664	0.82[JPT][hapmap];0.88[YRI][hapmap]
rs1498393	0.91[YRI][hapmap];0.86[AFR][1000 genomes]
rs1624678	0.86[AFR][1000 genomes]
rs1694577	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1694601	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1768666	0.82[JPT][hapmap];0.88[YRI][hapmap]
rs1768668	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1768672	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1768673	0.82[JPT][hapmap];0.88[YRI][hapmap]
rs2454326	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2486328	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2647435	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2647436	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2647437	0.86[AFR][1000 genomes]
rs2647459	0.95[CEU][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2647460	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2647463	0.82[LWK][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes]
rs2647468	0.81[AFR][1000 genomes]
rs2789795	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs2789796	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2789798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2789799	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427930	chr1:220120379-220333434	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	744 gene(s)	inside rSNPs	diseases
2	nsv998124	chr1:220132739-220189211	Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	n/a
3	nsv832636	chr1:220139697-220294352	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	738 gene(s)	inside rSNPs	diseases
4	esv1798515	chr1:220157811-220167371	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2254494	KCTD3	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220132800-220177000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:220140000-220167400	Weak transcription	Gastric	stomach
3	chr1:220140600-220162400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
4	chr1:220140600-220162400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr1:220140600-220163000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:220140800-220162400	Strong transcription	Fetal Intestine Large	intestine
7	chr1:220140800-220162400	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr1:220140800-220163200	Strong transcription	Primary T cells from cord blood	blood
9	chr1:220140800-220164000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:220140800-220173400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:220140800-220192400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:220141000-220163000	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:220141000-220163200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:220141000-220163400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:220141200-220162800	Strong transcription	Duodenum Mucosa	Duodenum
16	chr1:220141200-220163200	Strong transcription	HSMM	muscle
17	chr1:220141200-220192200	Weak transcription	Fetal Kidney	kidney
18	chr1:220141400-220162200	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr1:220141400-220162200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr1:220141400-220163400	Strong transcription	Dnd41	blood
21	chr1:220141400-220165400	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr1:220141600-220162200	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr1:220142200-220164000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr1:220142600-220169400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:220146400-220182800	Weak transcription	Spleen	Spleen
26	chr1:220147200-220169400	Weak transcription	Fetal Heart	heart
27	chr1:220147800-220163400	Strong transcription	K562	blood
28	chr1:220148200-220162200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr1:220148400-220162400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:220148600-220162200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:220149000-220167400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:220149200-220163400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:220149400-220162200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr1:220149400-220178200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr1:220149600-220166800	Weak transcription	Stomach Mucosa	stomach
36	chr1:220151200-220162200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr1:220151600-220162200	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr1:220153600-220169200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr1:220154200-220169200	Weak transcription	Fetal Brain Male	brain
40	chr1:220154400-220169200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:220154400-220169200	Weak transcription	Fetal Lung	lung
42	chr1:220154600-220166200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr1:220154600-220167000	Weak transcription	Aorta	Aorta
44	chr1:220154600-220169000	Weak transcription	Small Intestine	intestine
45	chr1:220154600-220169200	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr1:220154800-220167400	Weak transcription	Pancreas	Pancrea
47	chr1:220155000-220166000	Weak transcription	Brain Germinal Matrix	brain
48	chr1:220155600-220168600	Weak transcription	Brain Substantia Nigra	brain
49	chr1:220156000-220162200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr1:220156000-220163400	Strong transcription	NHEK	skin

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