Variant report

Variant	rs1379284
Chromosome Location	chr19:52071567-52071568
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr19:52071487-52071686	SH-SY5Y	brain:	n/a	n/a
2	TBL1XR1	chr19:52071248-52072020	K562	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:52071535-52071585	Hepatocyte	liver:	n/a
2	chr19:52071535-52071585	SKMC	muscle:	n/a
3	chr19:52071535-52071585	K562	blood:	n/a
4	chr19:52071535-52071585	CMK	blood:	n/a
5	chr19:52071535-52071585	HepG2	liver:	n/a
6	chr19:52071535-52071585	PANC-1	pancreas:	n/a
7	chr19:52071535-52071585	IMR90	lung:	fetal
8	chr19:52071535-52071585	HCF	heart:	n/a
9	chr19:52071535-52071585	HEK293	kidney:	embryo
10	chr19:52071535-52071585	U87	brain:	n/a
11	chr19:52071535-52071585	HIPEpiC	eye:	n/a
12	chr19:52071535-52071585	HAEpiC	amniotic membrane:	n/a
13	chr19:52071535-52071585	AG09319	gingival:	n/a
14	chr19:52071535-52071585	HUVEC	blood vessel:	n/a
15	chr19:52071535-52071585	Caco-2	colon:	n/a
16	chr19:52071535-52071585	HNPCEpiC	eye:	n/a
17	chr19:52071535-52071585	ovcar-3	ovarian:	n/a
18	chr19:52071535-52071585	SK-N-SH_RA	brain:	n/a
19	chr19:52071535-52071585	AG04449	skin:	fetal
20	chr19:52071535-52071585	NHDF-neo	bronchial:	n/a
21	chr19:52071535-52071585	AG09309	skin:	n/a
22	chr19:52071535-52071585	GM12878	blood:	n/a
23	chr19:52071535-52071585	ECC-1	luminal epithelium:	n/a
24	chr19:52071535-52071585	A549	lung:	n/a
25	chr19:52071535-52071585	HCPEpiC	choroid plexus:	n/a
26	chr19:52071535-52071585	AG10803	skin:	n/a
27	chr19:52071535-52071585	HPAEpiC	pulmonary alveolar:	n/a
28	chr19:52071535-52071585	SK-N-MC	brain:	n/a
29	chr19:52071535-52071585	LNCaP	prostate:	n/a
30	chr19:52071535-52071585	MCF10A-Er-Src	breast:	n/a
31	chr19:52071535-52071585	NHBE	bronchial:	n/a
32	chr19:52071535-52071585	H1-hESC	embryonic stem cell:	embryo
33	chr19:52071535-52071585	PFSK-1	brain:	n/a
34	chr19:52071535-52071585	GM19239	blood:	n/a
35	chr19:52071535-52071585	PrEC	prostate:	n/a
36	chr19:52071535-52071585	T-47D	breast:	n/a
37	chr19:52071535-52071585	NT2-D1	testis:	n/a
38	chr19:52071535-52071585	HCT-116	colon:	n/a
39	chr19:52071535-52071585	HCM	heart:	n/a
40	chr19:52071535-52071585	GM06990	blood:	n/a
41	chr19:52071535-52071585	AoSMC	blood vessel:	n/a
42	chr19:52071535-52071585	BE2_C	brain:	n/a
43	chr19:52071535-52071585	GM12892	blood:	n/a
44	chr19:52071535-52071585	HMEC	breast:	n/a
45	chr19:52071535-52071585	Hela-S3	cervix:	n/a
46	chr19:52071535-52071585	HRPEpiC	eye:	n/a
47	chr19:52071535-52071585	NH-A	brain:	n/a
48	chr19:52071535-52071585	HL-60	blood:	n/a
49	chr19:52071535-52071585	ProgFib	skin:	n/a
50	chr19:52071535-52071585	RPTEC	kidney:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:52048957..52051581-chr19:52070091..52071870,2	K562	blood:
2	chr19:51970546..51972983-chr19:52071317..52074312,2	K562	blood:
3	chr19:52008446..52010524-chr19:52071337..52074269,2	K562	blood:
4	chr19:52060227..52062359-chr19:52070779..52073037,2	K562	blood:
5	chr19:52054163..52056571-chr19:52069054..52071841,3	K562	blood:
6	chr19:52011237..52013383-chr19:52070576..52073278,2	K562	blood:

No data

Variant related genes	Relation type
ZNF175	TF binding region
SIGLEC29P	TF binding region
ZNF175	CpG island
SIGLEC29P	CpG island
ENSG00000268957	Chromatin interaction
ENSG00000268839	Chromatin interaction
ENSG00000269580	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1125620	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1585160	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16982846	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17453522	0.95[CEU][hapmap];0.94[JPT][hapmap];0.99[EUR][1000 genomes]
rs1962189	0.84[JPT][hapmap];0.82[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2305371	1.00[CEU][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2864106	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2864108	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2864109	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3752129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs3752132	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4308054	0.90[CHB][hapmap];0.90[JPT][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6509552	1.00[CEU][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7245838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7249641	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8102214	0.86[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs8108872	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8111685	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066308	chr19:51680133-52103974	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv544049	chr19:51680133-52103974	Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	nsv544051	chr19:51944903-52147459	Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	esv2758504	chr19:51991896-52266700	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	542 gene(s)	inside rSNPs	diseases
5	esv2758767	chr19:51991896-52604625	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	578 gene(s)	inside rSNPs	diseases
6	nsv469584	chr19:52001381-52151821	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv482654	chr19:52001381-52151821	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers 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 target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1379284	ZNF175	cis	Lymphoblastoid	GTEx
rs1379284	ZNF175	Cis_1M	lymphoblastoid	RTeQTL
rs1379284	ZNF175	cis	multi-tissue	Pritchard
rs1379284	ZNF175	cis	Esophagus Muscularis	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52067800-52073600	Enhancers	K562	blood
2	chr19:52069400-52073800	Weak transcription	Primary B cells from peripheral blood	blood
3	chr19:52069400-52074000	Weak transcription	GM12878-XiMat	blood
4	chr19:52070200-52074200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr19:52071200-52074000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr19:52071400-52074200	Weak transcription	Placenta	Placenta

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