Variant report

Variant	rs28374326
Chromosome Location	chr4:55143321-55143322
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr4:55143138-55143547	GM12878	blood:	n/a	chr4:55143248-55143259
2	POLR2A	chr4:55143227-55143323	HUVEC	blood vessel:	n/a	n/a
3	RELA	chr4:55143318-55144135	GM12878	blood:	n/a	n/a
4	RELA	chr4:55143270-55144354	GM12891	blood:	n/a	n/a
5	CTBP2	chr4:55143144-55143717	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:55143285-55143335	GM12891	blood:	n/a
2	chr4:55143285-55143335	ProgFib	skin:	n/a
3	chr4:55143285-55143335	HepG2	liver:	n/a
4	chr4:55143285-55143335	Hela-S3	cervix:	n/a
5	chr4:55143285-55143335	AoSMC	blood vessel:	n/a
6	chr4:55143285-55143335	PANC-1	pancreas:	n/a
7	chr4:55143285-55143335	AG04449	skin:	fetal
8	chr4:55143285-55143335	A549	lung:	n/a
9	chr4:55143285-55143335	ovcar-3	ovarian:	n/a
10	chr4:55143285-55143335	GM12892	blood:	n/a
11	chr4:55143285-55143335	CMK	blood:	n/a
12	chr4:55143285-55143335	NB4	blood:	n/a
13	chr4:55143285-55143335	MCF-7	breast:	n/a
14	chr4:55143285-55143335	HNPCEpiC	eye:	n/a
15	chr4:55143285-55143335	SK-N-MC	brain:	n/a
16	chr4:55143285-55143335	Caco-2	colon:	n/a
17	chr4:55143285-55143335	U87	brain:	n/a
18	chr4:55143285-55143335	NH-A	brain:	n/a
19	chr4:55143285-55143335	ECC-1	luminal epithelium:	n/a
20	chr4:55143285-55143335	HRE	kidney:	n/a
21	chr4:55143285-55143335	GM19239	blood:	n/a
22	chr4:55143285-55143335	NHDF-neo	bronchial:	n/a
23	chr4:55143285-55143335	HIPEpiC	eye:	n/a
24	chr4:55143285-55143335	AG04450	lung:	fetal
25	chr4:55143285-55143335	GM06990	blood:	n/a
26	chr4:55143285-55143335	BE2_C	brain:	n/a
27	chr4:55143285-55143335	Hepatocyte	liver:	n/a
28	chr4:55143285-55143335	BJ	skin:	n/a
29	chr4:55143285-55143335	AG10803	skin:	n/a
30	chr4:55143285-55143335	SK-N-SH_RA	brain:	n/a
31	chr4:55143285-55143335	AG09319	gingival:	n/a
32	chr4:55143285-55143335	H1-hESC	embryonic stem cell:	embryo
33	chr4:55143285-55143335	GM12878	blood:	n/a
34	chr4:55143285-55143335	RPTEC	kidney:	n/a
35	chr4:55143285-55143335	NT2-D1	testis:	n/a
36	chr4:55143285-55143335	HUVEC	blood vessel:	n/a
37	chr4:55143285-55143335	HEEpiC	esophagus:	n/a
38	chr4:55143285-55143335	PFSK-1	brain:	n/a
39	chr4:55143285-55143335	NHBE	bronchial:	n/a
40	chr4:55143285-55143335	MCF10A-Er-Src	breast:	n/a
41	chr4:55143285-55143335	HCPEpiC	choroid plexus:	n/a
42	chr4:55143285-55143335	HPAEpiC	pulmonary alveolar:	n/a
43	chr4:55143285-55143335	HCM	heart:	n/a
44	chr4:55143285-55143335	HMEC	breast:	n/a
45	chr4:55143285-55143335	K562	blood:	n/a
46	chr4:55143285-55143335	SAEC	small airway:	n/a
47	chr4:55143285-55143335	HCT-116	colon:	n/a
48	chr4:55143285-55143335	IMR90	lung:	fetal
49	chr4:55143285-55143335	HCF	heart:	n/a
50	chr4:55143285-55143335	SKMC	muscle:	n/a

No data

Variant related genes	Relation type
PDGFRA	TF binding region
PDGFRA	CpG island

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10003055	0.89[AMR][1000 genomes]
rs10004857	0.89[AMR][1000 genomes]
rs10010509	0.89[AMR][1000 genomes]
rs10020847	0.91[AMR][1000 genomes]
rs10021728	0.91[AMR][1000 genomes]
rs10028020	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10032688	0.89[AMR][1000 genomes]
rs1105825	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11133317	0.84[AMR][1000 genomes]
rs11733839	0.84[AMR][1000 genomes]
rs11931555	0.91[AMR][1000 genomes]
rs11935157	0.89[AMR][1000 genomes]
rs11940889	0.91[AMR][1000 genomes]
rs12505491	0.85[EUR][1000 genomes]
rs12506290	0.85[EUR][1000 genomes]
rs12508225	0.85[EUR][1000 genomes]
rs12641563	0.85[EUR][1000 genomes]
rs12644709	0.82[EUR][1000 genomes]
rs12644749	0.84[EUR][1000 genomes]
rs13147194	0.84[AMR][1000 genomes]
rs1547905	0.86[AMR][1000 genomes]
rs1565669	0.85[EUR][1000 genomes]
rs1565670	0.82[EUR][1000 genomes]
rs2228230	0.91[AMR][1000 genomes]
rs2229307	0.84[EUR][1000 genomes]
rs2276948	0.83[AMR][1000 genomes]
rs2307049	0.84[EUR][1000 genomes]
rs2307050	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2412556	0.87[AMR][1000 genomes]
rs2412557	0.87[AMR][1000 genomes]
rs2412558	0.88[AMR][1000 genomes]
rs28489067	0.85[EUR][1000 genomes]
rs28528897	0.85[EUR][1000 genomes]
rs28600756	0.85[EUR][1000 genomes]
rs28650939	0.86[EUR][1000 genomes]
rs28698464	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28811736	0.94[AMR][1000 genomes]
rs35597368	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3690	0.84[AMR][1000 genomes]
rs4289498	0.88[AMR][1000 genomes]
rs4358459	0.85[EUR][1000 genomes]
rs4864864	0.85[EUR][1000 genomes]
rs4864865	0.85[EUR][1000 genomes]
rs4864872	0.85[AMR][1000 genomes]
rs4864875	0.89[AMR][1000 genomes]
rs4864876	0.89[AMR][1000 genomes]
rs55732997	0.89[AMR][1000 genomes]
rs55784333	0.89[AMR][1000 genomes]
rs56145315	0.85[EUR][1000 genomes]
rs58435984	0.82[EUR][1000 genomes]
rs58727676	0.85[EUR][1000 genomes]
rs60218083	0.89[AMR][1000 genomes]
rs67279506	0.85[EUR][1000 genomes]
rs67388297	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67600360	0.85[EUR][1000 genomes]
rs6855761	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73252948	0.85[EUR][1000 genomes]
rs73252950	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7660560	0.85[EUR][1000 genomes]
rs7677708	0.87[AMR][1000 genomes]
rs7686588	0.85[EUR][1000 genomes]
rs7688997	0.85[EUR][1000 genomes]
rs7691129	0.85[EUR][1000 genomes]
rs9993187	0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008793	chr4:55060925-55535807	Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv537098	chr4:55060925-55535807	Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1004408	chr4:55124471-55179212	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
4	nsv537099	chr4:55124471-55179212	Genic enhancers Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv1001094	chr4:55131860-55189739	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55119400-55148000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:55121000-55147600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr4:55121000-55153200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr4:55121200-55147200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr4:55124400-55147800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr4:55131600-55148000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr4:55136600-55148600	Strong transcription	Fetal Lung	lung
8	chr4:55137000-55145600	Strong transcription	Fetal Stomach	stomach
9	chr4:55137400-55161600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr4:55138200-55148400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:55139000-55153000	Weak transcription	Fetal Kidney	kidney
12	chr4:55139600-55143800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr4:55139800-55148600	Genic enhancers	Osteobl	bone
14	chr4:55140000-55147200	Weak transcription	Esophagus	oesophagus
15	chr4:55140200-55149200	Weak transcription	Fetal Intestine Small	intestine
16	chr4:55140400-55149400	Genic enhancers	NHDF-Ad	bronchial
17	chr4:55140800-55144800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr4:55140800-55148600	Genic enhancers	NHLF	lung
19	chr4:55141200-55149000	Weak transcription	Placenta	Placenta
20	chr4:55141400-55144000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr4:55141600-55145600	Strong transcription	Fetal Muscle Leg	muscle
22	chr4:55141800-55147200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr4:55142000-55143600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr4:55142000-55145600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr4:55142000-55148200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr4:55142200-55143600	Genic enhancers	Aorta	Aorta
27	chr4:55142200-55143600	Enhancers	Fetal Brain Male	brain
28	chr4:55142200-55143600	Enhancers	Psoas Muscle	Psoas
29	chr4:55142200-55144400	Enhancers	Right Atrium	heart
30	chr4:55142400-55143800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr4:55142400-55144200	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr4:55142400-55144200	Enhancers	Right Ventricle	heart
33	chr4:55142600-55143600	Bivalent Enhancer	Brain Anterior Caudate	brain
34	chr4:55142600-55143600	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr4:55142600-55143800	Genic enhancers	Cortex derived primary cultured neurospheres	brain
36	chr4:55142600-55144400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
37	chr4:55142800-55143400	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
38	chr4:55142800-55143600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr4:55142800-55143600	Enhancers	Lung	lung
40	chr4:55142800-55143600	Flanking Active TSS	GM12878-XiMat	blood
41	chr4:55142800-55143800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr4:55142800-55143800	Flanking Active TSS	NHEK	skin
43	chr4:55142800-55144200	Enhancers	HMEC	breast
44	chr4:55142800-55144200	Enhancers	HSMMtube	muscle
45	chr4:55142800-55144400	Enhancers	Left Ventricle	heart
46	chr4:55142800-55144800	Enhancers	Pancreas	Pancrea
47	chr4:55142800-55146800	Genic enhancers	Ovary	ovary
48	chr4:55143000-55143400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr4:55143000-55143400	Weak transcription	Gastric	stomach
50	chr4:55143000-55143400	Weak transcription	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links