Variant report

Variant	rs1447610
Chromosome Location	chr3:160588285-160588286
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3AK20	chr3:160587364-160588321	MCF-7	breast:	n/a	n/a
2	CEBPB	chr3:160587553-160588418	Hela-S3	cervix:	n/a	chr3:160587930-160587942
3	FOS	chr3:160588282-160588466	MCF10A-Er-Src	breast:	n/a	chr3:160588288-160588297
4	KAP1	chr3:160587575-160588473	HEK293	kidney:	n/a	n/a
5	STAT3	chr3:160588266-160588466	MCF10A-Er-Src	breast:	n/a	chr3:160588380-160588391
6	TCF12	chr3:160587484-160588380	MCF-7	breast:	n/a	n/a
7	POLR2A	chr3:160587643-160588286	MCF10A-Er-Src	breast:	n/a	n/a
8	ATF1	chr3:160588178-160588432	K562	blood:	n/a	n/a
9	KAP1	chr3:160587482-160588485	U2OS	brain:	n/a	n/a
10	FOXA1	chr3:160588194-160588429	T-47D	breast:	n/a	n/a
11	TFAP2A	chr3:160587542-160588486	Hela-S3	cervix:	n/a	chr3:160587676-160587690 chr3:160587676-160587690 chr3:160587826-160587841

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:160588268-160588318	SKMC	muscle:	n/a
2	chr3:160588268-160588318	HCPEpiC	choroid plexus:	n/a
3	chr3:160588268-160588318	HNPCEpiC	eye:	n/a
4	chr3:160588268-160588318	BE2_C	brain:	n/a
5	chr3:160588268-160588318	HEEpiC	esophagus:	n/a
6	chr3:160588268-160588318	GM19239	blood:	n/a
7	chr3:160588268-160588318	CMK	blood:	n/a
8	chr3:160588268-160588318	AG10803	skin:	n/a
9	chr3:160588268-160588318	GM12891	blood:	n/a
10	chr3:160588268-160588318	AG04450	lung:	fetal
11	chr3:160588268-160588318	BJ	skin:	n/a
12	chr3:160588268-160588318	U87	brain:	n/a
13	chr3:160588268-160588318	LNCaP	prostate:	n/a
14	chr3:160588268-160588318	AoSMC	blood vessel:	n/a
15	chr3:160588268-160588318	AG09309	skin:	n/a
16	chr3:160588268-160588318	NT2-D1	testis:	n/a
17	chr3:160588268-160588318	RPTEC	kidney:	n/a
18	chr3:160588268-160588318	HEK293	kidney:	embryo
19	chr3:160588268-160588318	HRE	kidney:	n/a
20	chr3:160588268-160588318	NHBE	bronchial:	n/a
21	chr3:160588268-160588318	Hela-S3	cervix:	n/a
22	chr3:160588268-160588318	HCT-116	colon:	n/a
23	chr3:160588268-160588318	SAEC	small airway:	n/a
24	chr3:160588268-160588318	HMEC	breast:	n/a
25	chr3:160588268-160588318	HCM	heart:	n/a
26	chr3:160588268-160588318	SK-N-SH_RA	brain:	n/a
27	chr3:160588268-160588318	AG04449	skin:	fetal
28	chr3:160588268-160588318	AG09319	gingival:	n/a
29	chr3:160588268-160588318	PFSK-1	brain:	n/a
30	chr3:160588268-160588318	HRCEpiC	kidney:	n/a
31	chr3:160588268-160588318	MCF-7	breast:	n/a
32	chr3:160588268-160588318	NH-A	brain:	n/a
33	chr3:160588268-160588318	GM12892	blood:	n/a
34	chr3:160588268-160588318	Jurkat	blood:	n/a
35	chr3:160588268-160588318	PANC-1	pancreas:	n/a
36	chr3:160588268-160588318	GM06990	blood:	n/a
37	chr3:160588268-160588318	ProgFib	skin:	n/a
38	chr3:160588268-160588318	HAEpiC	amniotic membrane:	n/a
39	chr3:160588268-160588318	ECC-1	luminal epithelium:	n/a
40	chr3:160588268-160588318	ovcar-3	ovarian:	n/a
41	chr3:160588268-160588318	K562	blood:	n/a
42	chr3:160588268-160588318	Hepatocyte	liver:	n/a
43	chr3:160588268-160588318	Caco-2	colon:	n/a
44	chr3:160588268-160588318	HUVEC	blood vessel:	n/a
45	chr3:160588268-160588318	A549	lung:	n/a
46	chr3:160588268-160588318	IMR90	lung:	fetal
47	chr3:160588268-160588318	HepG2	liver:	n/a
48	chr3:160588268-160588318	PrEC	prostate:	n/a
49	chr3:160588268-160588318	HL-60	blood:	n/a
50	chr3:160588268-160588318	GM12878	blood:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160587600..160589495-chr3:161088974..161091016,2	MCF-7	breast:

No data

Variant related genes	Relation type
PPM1L	TF binding region
PPM1L	CpG island
ENSG00000196542	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10154889	0.95[CEU][hapmap]
rs10433352	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs11711152	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11713093	0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs11718966	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11916355	0.85[EUR][1000 genomes]
rs11922296	0.81[JPT][hapmap]
rs13071999	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13073059	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13315565	0.94[CEU][hapmap]
rs1345156	1.00[CEU][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs1348976	0.81[JPT][hapmap]
rs1374789	0.81[JPT][hapmap]
rs1374790	0.81[JPT][hapmap]
rs1447615	0.81[JPT][hapmap]
rs1447622	1.00[CEU][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1562464	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap]
rs16831563	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16831796	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs1839016	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1839018	0.81[JPT][hapmap]
rs1868105	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1868107	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1868108	0.80[CHD][hapmap]
rs1868109	0.81[JPT][hapmap]
rs1965186	0.81[TSI][hapmap]
rs2044571	1.00[CEU][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs2197700	0.90[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2889390	0.85[JPT][hapmap]
rs35257491	0.89[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4679920	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6441337	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6441338	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66872845	0.82[EUR][1000 genomes]
rs6768115	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6774725	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6801330	0.81[JPT][hapmap]
rs6801444	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs733948	0.81[MEX][hapmap]
rs7624185	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[GIH][hapmap];0.80[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap]
rs7628389	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs7641892	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs898677	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs935497	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs956447	0.81[JPT][hapmap]
rs964533	1.00[CEU][hapmap]
rs9812507	1.00[CEU][hapmap]
rs9822435	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs9832109	1.00[CEU][hapmap];0.80[MEX][hapmap];0.94[TSI][hapmap]
rs9844267	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9845943	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9857482	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9857855	0.84[CEU][hapmap]
rs9860537	1.00[CEU][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs9871801	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9876142	0.90[CEU][hapmap];0.81[GIH][hapmap];0.82[TSI][hapmap]
rs9881807	0.84[CHD][hapmap]
rs9883566	0.90[CEU][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap];0.85[TSI][hapmap]

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	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1009249	chr3:160496237-160627378	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv536780	chr3:160496237-160627378	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv32963	chr3:160555238-160603116	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1447610	B3GALNT1	cis	lymphoblastoid	seeQTL
rs1447610	PPM1L	cis	cerebellum	SCAN
rs1447610	SPTSSB	cis	Thyroid	GTEx
rs1447610	C3orf57	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160587400-160593000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:160587600-160588400	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr3:160587600-160588400	Enhancers	Liver	Liver
4	chr3:160587600-160588800	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr3:160587800-160588400	Enhancers	H9 Cell Line	embryonic stem cell
6	chr3:160587800-160588400	Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr3:160587800-160588400	Active TSS	Stomach Smooth Muscle	stomach
8	chr3:160587800-160588600	Enhancers	Brain Anterior Caudate	brain
9	chr3:160587800-160588600	Active TSS	Right Ventricle	heart
10	chr3:160587800-160588600	Active TSS	Skeletal Muscle Male	skeletal muscle
11	chr3:160587800-160589000	Enhancers	Brain Germinal Matrix	brain
12	chr3:160587800-160589000	Enhancers	Colon Smooth Muscle	Colon
13	chr3:160588000-160588400	Active TSS	Fetal Muscle Leg	muscle
14	chr3:160588000-160588400	Active TSS	HSMMtube	muscle
15	chr3:160588000-160588600	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr3:160588000-160588600	Active TSS	Psoas Muscle	Psoas
17	chr3:160588000-160588600	Active TSS	Right Atrium	heart
18	chr3:160588200-160588400	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr3:160588200-160588400	Enhancers	Left Ventricle	heart
20	chr3:160588200-160588400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr3:160588200-160588400	Enhancers	Hela-S3	cervix
22	chr3:160588200-160594000	Weak transcription	Fetal Heart	heart
23	chr3:160588200-160594400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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