Variant report

Variant	rs4382766
Chromosome Location	chr1:173445076-173445077
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:50)
CpG islands
(count:61)
Chromatin interactive
region (count:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr1:173444862-173445344	K562	blood:	n/a	chr1:173445056-173445067 chr1:173445057-173445067 chr1:173445057-173445067
2	FOS	chr1:173444797-173445874	MCF10A-Er-Src	breast:	n/a	chr1:173445057-173445067 chr1:173445057-173445067
3	POLR2A	chr1:173444833-173445208	SK-N-SH	brain:	n/a	n/a
4	E2F4	chr1:173444740-173445160	MCF10A-Er-Src	breast:	n/a	n/a
5	RCOR1	chr1:173445057-173445137	HepG2	liver:	n/a	n/a
6	FOS	chr1:173444795-173445297	MCF10A-Er-Src	breast:	n/a	chr1:173445057-173445067 chr1:173445057-173445067
7	SIN3AK20	chr1:173444849-173445481	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr1:173444908-173445115	Hela-S3	cervix:	n/a	n/a
9	ZKSCAN1	chr1:173444907-173447574	Hela-S3	cervix:	n/a	n/a
10	CBX3	chr1:173444903-173446307	K562	blood:	n/a	chr1:173444947-173444958
11	MXI1	chr1:173444253-173448100	IMR90	lung:	n/a	chr1:173447831-173447846
12	BHLHE40	chr1:173444953-173447722	K562	blood:	n/a	chr1:173446795-173446811
13	MYC	chr1:173444874-173445207	MCF10A-Er-Src	breast:	n/a	n/a
14	MYC	chr1:173444793-173445230	MCF10A-Er-Src	breast:	n/a	n/a
15	ARID3A	chr1:173444969-173445236	K562	blood:	n/a	n/a
16	FOS	chr1:173444872-173445231	MCF10A-Er-Src	breast:	n/a	chr1:173445057-173445067 chr1:173445057-173445067
17	MAX	chr1:173445044-173447710	Hela-S3	cervix:	n/a	n/a
18	USF2	chr1:173444976-173446389	Hela-S3	cervix:	n/a	n/a
19	KAP1	chr1:173444758-173446206	HEK293	kidney:	n/a	n/a
20	CTCF	chr1:173445060-173445210	AoAF	blood vessel:	n/a	n/a
21	RCOR1	chr1:173444919-173445355	K562	blood:	n/a	n/a
22	JUND	chr1:173444965-173445210	HepG2	liver:	n/a	chr1:173445056-173445067 chr1:173445057-173445067 chr1:173445057-173445067
23	SMC3	chr1:173444910-173448008	Hela-S3	cervix:	n/a	n/a
24	MAFK	chr1:173444913-173445414	Hela-S3	cervix:	n/a	n/a
25	HEY1	chr1:173444814-173445154	HepG2	liver:	n/a	n/a
26	FOXA1	chr1:173444735-173445230	HepG2	liver:	n/a	n/a
27	FOS	chr1:173444859-173445479	MCF10A-Er-Src	breast:	n/a	chr1:173445057-173445067 chr1:173445057-173445067
28	RFX5	chr1:173444951-173445433	Hela-S3	cervix:	n/a	n/a
29	JUN	chr1:173444105-173448462	K562	blood:	n/a	chr1:173446953-173446961 chr1:173445057-173445067 chr1:173447039-173447048 chr1:173445057-173445067
30	EP300	chr1:173444878-173445682	K562	blood:	n/a	chr1:173445337-173445353
31	HCFC1	chr1:173444740-173448059	Hela-S3	cervix:	n/a	n/a
32	STAT3	chr1:173444839-173445122	MCF10A-Er-Src	breast:	n/a	n/a
33	RAD21	chr1:173444857-173445298	Hela-S3	cervix:	n/a	n/a
34	CEBPB	chr1:173444811-173445362	Hela-S3	cervix:	n/a	n/a
35	TBP	chr1:173444894-173445420	Hela-S3	cervix:	n/a	n/a
36	GTF2F1	chr1:173444906-173447824	Hela-S3	cervix:	n/a	n/a
37	CEBPB	chr1:173444884-173445441	IMR90	lung:	n/a	n/a
38	MAX	chr1:173444772-173445472	SK-N-SH	brain:	n/a	n/a
39	ARID3A	chr1:173444869-173445404	HepG2	liver:	n/a	n/a
40	MXI1	chr1:173444135-173448173	SK-N-SH	brain:	n/a	chr1:173447831-173447846
41	STAT3	chr1:173444825-173445171	MCF10A-Er-Src	breast:	n/a	n/a
42	MAZ	chr1:173444567-173447830	IMR90	lung:	n/a	n/a
43	MAFK	chr1:173444913-173445166	IMR90	lung:	n/a	n/a
44	FOSL2	chr1:173444832-173445370	SK-N-SH	brain:	n/a	chr1:173445057-173445067 chr1:173445057-173445067
45	POLR2A	chr1:173444928-173445443	HepG2	liver:	n/a	n/a
46	GATA2	chr1:173444874-173446246	SH-SY5Y	brain:	n/a	chr1:173445349-173445356
47	POLR2A	chr1:173444798-173445207	MCF10A-Er-Src	breast:	n/a	n/a
48	MYC	chr1:173444955-173445281	K562	blood:	n/a	n/a
49	STAT3	chr1:173444799-173445160	MCF10A-Er-Src	breast:	n/a	n/a
50	STAT3	chr1:173444805-173445240	MCF10A-Er-Src	breast:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:173445043-173445093	NHDF-neo	bronchial:	n/a
2	chr1:173445043-173445093	HCT-116	colon:	n/a
3	chr1:173445043-173445093	SK-N-SH	brain:	n/a
4	chr1:173445043-173445093	SK-N-SH_RA	brain:	n/a
5	chr1:173445043-173445093	Hepatocyte	liver:	n/a
6	chr1:173445043-173445093	K562	blood:	n/a
7	chr1:173445043-173445093	MCF10A-Er-Src	breast:	n/a
8	chr1:173445043-173445093	HNPCEpiC	eye:	n/a
9	chr1:173445043-173445093	Hela-S3	cervix:	n/a
10	chr1:173445043-173445093	U87	brain:	n/a
11	chr1:173445043-173445093	NB4	blood:	n/a
12	chr1:173445043-173445093	BE2_C	brain:	n/a
13	chr1:173445043-173445093	ovcar-3	ovarian:	n/a
14	chr1:173445043-173445093	NT2-D1	testis:	n/a
15	chr1:173445043-173445093	SK-N-MC	brain:	n/a
16	chr1:173445043-173445093	AG04449	skin:	fetal
17	chr1:173445043-173445093	PANC-1	pancreas:	n/a
18	chr1:173445043-173445093	Jurkat	blood:	n/a
19	chr1:173445043-173445093	HCPEpiC	choroid plexus:	n/a
20	chr1:173445043-173445093	RPTEC	kidney:	n/a
21	chr1:173445043-173445093	IMR90	lung:	fetal
22	chr1:173445043-173445093	GM12892	blood:	n/a
23	chr1:173445043-173445093	HMEC	breast:	n/a
24	chr1:173445043-173445093	HIPEpiC	eye:	n/a
25	chr1:173445043-173445093	AG09319	gingival:	n/a
26	chr1:173445043-173445093	AG09309	skin:	n/a
27	chr1:173445043-173445093	AG10803	skin:	n/a
28	chr1:173445043-173445093	ECC-1	luminal epithelium:	n/a
29	chr1:173445043-173445093	HCF	heart:	n/a
30	chr1:173445043-173445093	HCM	heart:	n/a
31	chr1:173445043-173445093	LNCaP	prostate:	n/a
32	chr1:173445043-173445093	GM19239	blood:	n/a
33	chr1:173445043-173445093	HEEpiC	esophagus:	n/a
34	chr1:173445043-173445093	AG04450	lung:	fetal
35	chr1:173445043-173445093	HRPEpiC	eye:	n/a
36	chr1:173445043-173445093	BJ	skin:	n/a
37	chr1:173445043-173445093	HRE	kidney:	n/a
38	chr1:173445043-173445093	HPAEpiC	pulmonary alveolar:	n/a
39	chr1:173445043-173445093	HepG2	liver:	n/a
40	chr1:173445043-173445093	PFSK-1	brain:	n/a
41	chr1:173445043-173445093	PrEC	prostate:	n/a
42	chr1:173445043-173445093	NHBE	bronchial:	n/a
43	chr1:173445043-173445093	GM06990	blood:	n/a
44	chr1:173445043-173445093	HRCEpiC	kidney:	n/a
45	chr1:173445043-173445093	CMK	blood:	n/a
46	chr1:173445043-173445093	Caco-2	colon:	n/a
47	chr1:173445043-173445093	HL-60	blood:	n/a
48	chr1:173445043-173445093	GM12878	blood:	n/a
49	chr1:173445043-173445093	SKMC	muscle:	n/a
50	chr1:173445043-173445093	NH-A	brain:	n/a

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:173444743..173447866-chr1:173792301..173795321,5	MCF-7	breast:
2	chr1:173442552..173449186-chr1:173835087..173838637,8	MCF-7	breast:
3	chr1:173444678..173448018-chr1:173835571..173838629,5	K562	blood:
4	chr1:173442536..173447801-chr1:173833439..173838851,7	K562	blood:
5	chr1:173444899..173448691-chr1:173990820..173993753,4	MCF-7	breast:
6	chr1:173443316..173450639-chr1:173791413..173797919,15	K562	blood:
7	chr1:173443428..173450639-chr1:173791407..173797248,10	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PRDX6-2	chr1:173444952-173445375	NONHSAT007638

No data

Variant related genes	Relation type
PRDX6	TF binding region
PRDX6	CpG island
ENSG00000234741	Chromatin interaction
ENSG00000120334	Chromatin interaction
ENSG00000224977	Chromatin interaction
ENSG00000185278	Chromatin interaction
ENSG00000117593	Chromatin interaction
ENSG00000208317	Chromatin interaction
ENSG00000135870	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10753081	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753082	0.82[AFR][1000 genomes]
rs10753083	0.82[YRI][hapmap]
rs10798282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10912617	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10912618	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10912656	0.82[CHB][hapmap]
rs12075314	0.85[AFR][1000 genomes]
rs12077271	0.87[AFR][1000 genomes]
rs12080722	0.81[AFR][1000 genomes]
rs12092383	0.81[CHB][hapmap]
rs12140760	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs12565753	0.83[AFR][1000 genomes]
rs12745058	0.89[AFR][1000 genomes]
rs1359460	0.94[LWK][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes]
rs1547154	0.84[AFR][1000 genomes]
rs1886638	0.82[YRI][hapmap]
rs4255417	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4276950	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4325171	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4611	0.92[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4916220	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4916355	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4916358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4916359	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4916361	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4916362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4916363	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4916366	0.85[AFR][1000 genomes]
rs4916367	0.85[AFR][1000 genomes]
rs55654074	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6425231	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6425233	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6696012	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6702835	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7314	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7516544	0.85[AFR][1000 genomes]
rs7535963	0.85[AFR][1000 genomes]
rs7537938	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7540065	0.93[ASW][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs7551305	0.83[AFR][1000 genomes]
rs7556003	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs912768	0.85[LWK][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes]
rs9425718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9425719	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9425723	0.95[ASN][1000 genomes]
rs9425724	0.96[AFR][1000 genomes];0.95[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	nsv831915	chr1:173268424-173482157	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4382766	GPR52	cis	parietal	SCAN
rs4382766	PRDX6	cis	parietal	SCAN
rs4382766	FASLG	cis	cerebellum	SCAN
rs4382766	TNFSF4	cis	parietal	SCAN
rs4382766	DARS2	cis	cerebellum	SCAN
rs4382766	TNFSF18	cis	parietal	SCAN
rs4382766	SLC9A11	cis	parietal	SCAN
rs4382766	PRDX6	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173440400-173445200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:173440600-173445200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:173440600-173445200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:173440600-173445800	Weak transcription	Spleen	Spleen
5	chr1:173441400-173445200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr1:173441600-173445200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:173442400-173445200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr1:173442400-173445200	Enhancers	Fetal Intestine Large	intestine
9	chr1:173442400-173445200	Enhancers	Fetal Intestine Small	intestine
10	chr1:173442400-173445200	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr1:173443200-173445200	Weak transcription	Ovary	ovary
12	chr1:173443600-173445200	Enhancers	Placenta Amnion	Placenta Amnion
13	chr1:173443600-173445200	Active TSS	HepG2	liver
14	chr1:173443600-173445800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
15	chr1:173443600-173447400	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr1:173443600-173447800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:173443800-173445200	Weak transcription	Aorta	Aorta
18	chr1:173443800-173445200	Enhancers	Esophagus	oesophagus
19	chr1:173443800-173445400	Weak transcription	Fetal Kidney	kidney
20	chr1:173443800-173447600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:173444000-173445400	Flanking Active TSS	Stomach Smooth Muscle	stomach
22	chr1:173444000-173448000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr1:173444200-173445200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr1:173444200-173445200	Enhancers	Small Intestine	intestine
25	chr1:173444200-173445400	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr1:173444200-173445600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:173444200-173445600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
28	chr1:173444200-173445800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr1:173444200-173445800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:173444200-173446000	Flanking Active TSS	Liver	Liver
31	chr1:173444200-173447400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:173444200-173447400	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr1:173444400-173445200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:173444400-173445200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:173444400-173445200	Active TSS	Brain Inferior Temporal Lobe	brain
36	chr1:173444400-173445200	Enhancers	Fetal Lung	lung
37	chr1:173444400-173445200	Active TSS	Fetal Muscle Leg	muscle
38	chr1:173444400-173445200	Enhancers	Fetal Stomach	stomach
39	chr1:173444400-173445200	Active TSS	Right Ventricle	heart
40	chr1:173444400-173445200	Active TSS	HSMM	muscle
41	chr1:173444400-173445200	Active TSS	NHDF-Ad	bronchial
42	chr1:173444400-173445200	Active TSS	NHLF	lung
43	chr1:173444400-173445400	Flanking Active TSS	Brain Anterior Caudate	brain
44	chr1:173444400-173445600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr1:173444400-173445600	Flanking Active TSS	NH-A	brain
46	chr1:173444400-173445600	Flanking Active TSS	Osteobl	bone
47	chr1:173444400-173445800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:173444400-173445800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
49	chr1:173444400-173446200	Flanking Active TSS	Duodenum Mucosa	Duodenum
50	chr1:173444400-173448600	Active TSS	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links