Variant report

Variant	rs2307050
Chromosome Location	chr4:55141293-55141294
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr4:55141265-55141650	GM12878	blood:	n/a	chr4:55141494-55141503

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:55139472..55141383-chr4:55141730..55143677,2	MCF-7	breast:
2	chr4:55135740..55138560-chr4:55139917..55141829,2	MCF-7	breast:

Variant related genes	Relation type
PDGFRA	TF binding region
ENSG00000134853	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10020847	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs10021728	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs10028020	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10032688	0.82[CHB][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap]
rs1105825	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11133317	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs11733839	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs12505491	0.85[EUR][1000 genomes]
rs12506290	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs12508225	0.85[EUR][1000 genomes]
rs12641563	0.83[CEU][hapmap];0.80[JPT][hapmap];0.85[EUR][1000 genomes]
rs12644709	0.81[CEU][hapmap];0.80[JPT][hapmap];0.82[EUR][1000 genomes]
rs12644749	0.84[EUR][1000 genomes]
rs13147194	0.82[CHB][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs1547904	0.91[CHB][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap]
rs1547905	0.91[CHB][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes]
rs1565669	0.85[EUR][1000 genomes]
rs1565670	0.82[EUR][1000 genomes]
rs2228230	0.82[CHB][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap]
rs2229307	0.83[CEU][hapmap];0.80[JPT][hapmap];0.84[EUR][1000 genomes]
rs2307049	0.83[CEU][hapmap];0.81[GIH][hapmap];0.80[JPT][hapmap];0.84[EUR][1000 genomes]
rs2412556	0.81[ASN][1000 genomes]
rs2412557	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs28374326	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][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	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28811736	0.81[AMR][1000 genomes]
rs35597368	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3690	0.82[CHB][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap]
rs3733540	0.82[CHB][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap]
rs4289498	0.91[CHB][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.81[ASN][1000 genomes]
rs4358459	0.83[CEU][hapmap];0.81[GIH][hapmap];0.80[JPT][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs4864862	0.80[JPT][hapmap]
rs4864864	0.85[EUR][1000 genomes]
rs4864865	0.85[EUR][1000 genomes]
rs4864872	0.82[CHB][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap]
rs4864876	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs56145315	0.85[EUR][1000 genomes]
rs58435984	0.82[EUR][1000 genomes]
rs58727676	0.85[EUR][1000 genomes]
rs67279506	0.85[EUR][1000 genomes]
rs67388297	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67600360	0.85[EUR][1000 genomes]
rs6836215	0.85[JPT][hapmap]
rs6850748	0.80[JPT][hapmap]
rs6855761	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73252948	0.85[EUR][1000 genomes]
rs73252950	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7660560	0.83[CEU][hapmap];0.81[GIH][hapmap];0.80[JPT][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs7677708	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs7677751	0.80[JPT][hapmap];0.95[MEX][hapmap]
rs7678144	0.80[JPT][hapmap]
rs7686588	0.83[CEU][hapmap];0.80[JPT][hapmap];0.85[EUR][1000 genomes]
rs7688997	0.83[CEU][hapmap];0.81[GIH][hapmap];0.80[JPT][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs7691129	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs9993187	0.86[JPT][hapmap]

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:49 , 50 per page) page: 1

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	chr4:55122400-55142600	Strong transcription	Cortex derived primary cultured neurospheres	brain
6	chr4:55124400-55147800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr4:55129200-55142400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr4:55130200-55142800	Weak transcription	Gastric	stomach
9	chr4:55130200-55143000	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr4:55130600-55142400	Weak transcription	Right Ventricle	heart
11	chr4:55131600-55148000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr4:55132200-55142200	Weak transcription	Liver	Liver
13	chr4:55132400-55142800	Weak transcription	Adipose Nuclei	Adipose
14	chr4:55133200-55143200	Strong transcription	Fetal Muscle Trunk	muscle
15	chr4:55133400-55143000	Weak transcription	Colonic Mucosa	Colon
16	chr4:55135000-55141400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr4:55135600-55142200	Weak transcription	Fetal Brain Male	brain
18	chr4:55136600-55148600	Strong transcription	Fetal Lung	lung
19	chr4:55136800-55142000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr4:55137000-55141800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr4:55137000-55142800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr4:55137000-55145600	Strong transcription	Fetal Stomach	stomach
23	chr4:55137400-55161600	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr4:55137600-55142400	Weak transcription	Fetal Intestine Large	intestine
25	chr4:55138200-55148400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr4:55138400-55143200	Weak transcription	HSMM	muscle
27	chr4:55139000-55153000	Weak transcription	Fetal Kidney	kidney
28	chr4:55139600-55142800	Weak transcription	NH-A	brain
29	chr4:55139600-55143800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr4:55139800-55148600	Genic enhancers	Osteobl	bone
31	chr4:55140000-55142400	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr4:55140000-55147200	Weak transcription	Esophagus	oesophagus
33	chr4:55140200-55149200	Weak transcription	Fetal Intestine Small	intestine
34	chr4:55140400-55142800	Weak transcription	Lung	lung
35	chr4:55140400-55149400	Genic enhancers	NHDF-Ad	bronchial
36	chr4:55140600-55142000	Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr4:55140600-55143000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr4:55140800-55141600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr4:55140800-55142800	Weak transcription	Left Ventricle	heart
40	chr4:55140800-55143200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr4:55140800-55144800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr4:55140800-55148600	Genic enhancers	NHLF	lung
43	chr4:55141000-55142000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr4:55141200-55141600	Weak transcription	Fetal Muscle Leg	muscle
45	chr4:55141200-55142200	Weak transcription	Aorta	Aorta
46	chr4:55141200-55142200	Weak transcription	Psoas Muscle	Psoas
47	chr4:55141200-55142200	Weak transcription	Right Atrium	heart
48	chr4:55141200-55142800	Strong transcription	Ovary	ovary
49	chr4:55141200-55149000	Weak transcription	Placenta	Placenta

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