Variant report

Variant	rs12120556
Chromosome Location	chr1:172115154-172115155
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr1:172113326-172116098	SK-N-SH	brain:	n/a	chr1:172114172-172114182
2	STAT3	chr1:172115097-172115294	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr1:172113262-172115212	SK-N-SH	brain:	n/a	n/a
4	PBX3	chr1:172113607-172115284	SK-N-SH	brain:	n/a	n/a
5	TEAD4	chr1:172113648-172115285	SK-N-SH	brain:	n/a	n/a
6	PBX3	chr1:172113653-172115247	SK-N-SH	brain:	n/a	n/a
7	JUND	chr1:172113635-172115583	SK-N-SH	brain:	n/a	chr1:172114009-172114018
8	GATA3	chr1:172113581-172115930	SK-N-SH	brain:	n/a	chr1:172114172-172114182
9	TCF12	chr1:172113270-172116247	SK-N-SH	brain:	n/a	chr1:172115875-172115882 chr1:172115810-172115819
10	NFIC	chr1:172113457-172115289	SK-N-SH	brain:	n/a	n/a
11	EP300	chr1:172113718-172115165	SK-N-SH_RA	brain:	n/a	chr1:172115114-172115128
12	TCF12	chr1:172113511-172116123	SK-N-SH	brain:	n/a	chr1:172115875-172115882 chr1:172115810-172115819
13	EP300	chr1:172113516-172115257	SK-N-SH	brain:	n/a	chr1:172115114-172115128

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:172115154-172115204	GM12892	blood:	n/a
2	chr1:172115154-172115204	HIPEpiC	eye:	n/a
3	chr1:172115154-172115204	NH-A	brain:	n/a
4	chr1:172115154-172115204	Hela-S3	cervix:	n/a
5	chr1:172115154-172115204	U87	brain:	n/a
6	chr1:172115154-172115204	Hepatocyte	liver:	n/a
7	chr1:172115154-172115204	K562	blood:	n/a
8	chr1:172115154-172115204	T-47D	breast:	n/a
9	chr1:172115154-172115204	AG09309	skin:	n/a
10	chr1:172115154-172115204	CMK	blood:	n/a
11	chr1:172115154-172115204	GM06990	blood:	n/a
12	chr1:172115154-172115204	AoSMC	blood vessel:	n/a
13	chr1:172115154-172115204	HRCEpiC	kidney:	n/a
14	chr1:172115154-172115204	HCM	heart:	n/a
15	chr1:172115154-172115204	HepG2	liver:	n/a
16	chr1:172115154-172115204	ovcar-3	ovarian:	n/a
17	chr1:172115154-172115204	HCPEpiC	choroid plexus:	n/a
18	chr1:172115154-172115204	HEEpiC	esophagus:	n/a
19	chr1:172115154-172115204	GM12878	blood:	n/a
20	chr1:172115154-172115204	ECC-1	luminal epithelium:	n/a
21	chr1:172115154-172115204	HCT-116	colon:	n/a
22	chr1:172115154-172115204	BJ	skin:	n/a
23	chr1:172115154-172115204	PFSK-1	brain:	n/a
24	chr1:172115154-172115204	NT2-D1	testis:	n/a
25	chr1:172115154-172115204	HMEC	breast:	n/a
26	chr1:172115154-172115204	SK-N-MC	brain:	n/a
27	chr1:172115154-172115204	LNCaP	prostate:	n/a
28	chr1:172115154-172115204	HCF	heart:	n/a
29	chr1:172115154-172115204	AG04450	lung:	fetal
30	chr1:172115154-172115204	NHBE	bronchial:	n/a
31	chr1:172115154-172115204	SK-N-SH_RA	brain:	n/a
32	chr1:172115154-172115204	A549	lung:	n/a
33	chr1:172115154-172115204	GM12891	blood:	n/a
34	chr1:172115154-172115204	IMR90	lung:	fetal
35	chr1:172115154-172115204	HRPEpiC	eye:	n/a
36	chr1:172115154-172115204	HAEpiC	amniotic membrane:	n/a
37	chr1:172115154-172115204	HEK293	kidney:	embryo
38	chr1:172115154-172115204	PANC-1	pancreas:	n/a
39	chr1:172115154-172115204	AG10803	skin:	n/a
40	chr1:172115154-172115204	BE2_C	brain:	n/a
41	chr1:172115154-172115204	H1-hESC	embryonic stem cell:	embryo
42	chr1:172115154-172115204	NHDF-neo	bronchial:	n/a
43	chr1:172115154-172115204	HUVEC	blood vessel:	n/a
44	chr1:172115154-172115204	SK-N-SH	brain:	n/a
45	chr1:172115154-172115204	NB4	blood:	n/a
46	chr1:172115154-172115204	RPTEC	kidney:	n/a
47	chr1:172115154-172115204	HL-60	blood:	n/a
48	chr1:172115154-172115204	SAEC	small airway:	n/a
49	chr1:172115154-172115204	HRE	kidney:	n/a
50	chr1:172115154-172115204	ProgFib	skin:	n/a

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:172114639..172117543-chr1:172117607..172120253,2	K562	blood:

No data

Variant related genes	Relation type
MIR199A2	TF binding region
DNM3OS	TF binding region
DNM3OS	CpG island
MIR199A2	CpG island

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10218612	1.00[JPT][hapmap]
rs10442603	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10489730	0.94[JPT][hapmap]
rs10797719	0.94[JPT][hapmap]
rs10797735	0.94[JPT][hapmap]
rs10797791	1.00[CEU][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs10910966	0.94[JPT][hapmap]
rs10911101	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10911109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10911110	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10911111	0.88[CEU][hapmap];0.95[EUR][1000 genomes]
rs10911112	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10911116	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs10911121	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];0.88[JPT][hapmap];0.87[MEX][hapmap];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10911122	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10911123	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10911124	0.94[CEU][hapmap]
rs10911125	0.94[CEU][hapmap]
rs12047492	1.00[CEU][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12141278	0.95[EUR][1000 genomes]
rs1475230	0.94[CEU][hapmap]
rs1475231	0.94[CEU][hapmap]
rs1555383	0.94[JPT][hapmap]
rs2038481	0.94[JPT][hapmap]
rs2057302	0.94[JPT][hapmap]
rs2146901	1.00[CEU][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes]
rs2181624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2208367	0.94[JPT][hapmap]
rs2295610	0.94[JPT][hapmap]
rs2295611	0.94[JPT][hapmap]
rs2421986	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2421987	1.00[CEU][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes]
rs3736791	0.94[JPT][hapmap]
rs4076678	0.94[JPT][hapmap]
rs4604727	0.94[CEU][hapmap];0.92[EUR][1000 genomes]
rs6425599	0.94[JPT][hapmap]
rs6669406	0.94[JPT][hapmap]
rs72719075	0.85[EUR][1000 genomes]
rs733190	0.83[CHD][hapmap]
rs7518865	0.94[JPT][hapmap]
rs7530970	0.94[JPT][hapmap]
rs9286842	0.94[JPT][hapmap]

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	nsv532342	chr1:171922237-172133785	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12120556	TNFSF4	cis	parietal	SCAN
rs12120556	TNFSF18	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172109800-172115200	Active TSS	Colon Smooth Muscle	Colon
2	chr1:172113600-172115600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:172113600-172116000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:172113800-172115200	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr1:172113800-172115400	Weak transcription	HMEC	breast
6	chr1:172113800-172115600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:172113800-172115800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:172113800-172117800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:172114000-172115600	Enhancers	Stomach Mucosa	stomach
10	chr1:172114200-172115200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:172114200-172115200	Enhancers	Fetal Heart	heart
12	chr1:172114200-172115200	Flanking Active TSS	Fetal Lung	lung
13	chr1:172114200-172115400	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr1:172114200-172115600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:172114200-172115600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
16	chr1:172114400-172115200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr1:172114400-172115200	Flanking Active TSS	Fetal Kidney	kidney
18	chr1:172114400-172115200	Flanking Active TSS	Osteobl	bone
19	chr1:172114400-172137000	Weak transcription	Brain Angular Gyrus	brain
20	chr1:172114600-172115200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:172114600-172115200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:172114600-172115600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:172114600-172115600	Enhancers	HUVEC	blood vessel
24	chr1:172114800-172115200	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr1:172114800-172115200	Enhancers	Rectal Smooth Muscle	rectum
26	chr1:172114800-172115200	Flanking Active TSS	NHDF-Ad	bronchial
27	chr1:172114800-172115600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:172114800-172115800	Enhancers	Fetal Intestine Small	intestine
29	chr1:172114800-172116200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr1:172114800-172117800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:172114800-172117800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:172114800-172118200	Enhancers	NHEK	skin
33	chr1:172114800-172123600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:172115000-172115400	Weak transcription	Duodenum Mucosa	Duodenum
35	chr1:172115000-172116000	Enhancers	NH-A	brain
36	chr1:172115000-172116400	Enhancers	Fetal Stomach	stomach
37	chr1:172115000-172116600	Enhancers	NHLF	lung
38	chr1:172115000-172117600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:172115000-172118000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr1:172115000-172119600	Weak transcription	Ovary	ovary
41	chr1:172115000-172119800	Weak transcription	Fetal Muscle Leg	muscle
42	chr1:172115000-172123400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:172115000-172123600	Weak transcription	Adipose Nuclei	Adipose
44	chr1:172115000-172133800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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