Variant report

Variant	rs4604142
Chromosome Location	chr5:60642595-60642596
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	CHD1	chr5:60641947-60643826	IMR90	lung:	n/a	n/a
2	POLR2A	chr5:60642154-60643716	IMR90	lung:	n/a	n/a
3	POLR2A	chr5:60642217-60642670	A549	lung:	n/a	n/a
4	CTCF	chr5:60642563-60642599	GM20000	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:60626862..60630406-chr5:60642263..60646074,4	MCF-7	breast:
2	chr5:60456802..60459800-chr5:60641121..60644130,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000251682	TF binding region
ENSG00000251279	Chromatin interaction
ENSG00000188725	Chromatin interaction
ENSG00000130449	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10041978	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1045352	0.80[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs10939900	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10939901	1.00[ASN][1000 genomes]
rs10939902	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10939903	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10939905	0.80[ASN][1000 genomes]
rs11742658	0.80[ASN][1000 genomes]
rs11743711	0.88[ASN][1000 genomes]
rs11747564	0.80[ASN][1000 genomes]
rs11749200	0.80[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs11750589	0.99[ASN][1000 genomes]
rs11950318	0.84[ASN][1000 genomes]
rs11952146	0.80[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs11954430	0.82[ASN][1000 genomes]
rs11954859	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12187112	0.94[ASN][1000 genomes]
rs12188627	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12189001	1.00[ASN][1000 genomes]
rs12518479	1.00[ASN][1000 genomes]
rs12520628	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12522647	0.86[ASN][1000 genomes]
rs12523278	0.83[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs13156100	0.80[ASN][1000 genomes]
rs13157657	0.82[ASN][1000 genomes]
rs13157831	0.80[ASN][1000 genomes]
rs13158675	1.00[ASN][1000 genomes]
rs13160801	0.82[ASN][1000 genomes]
rs13162358	1.00[ASN][1000 genomes]
rs13163970	0.82[ASN][1000 genomes]
rs13169711	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13170135	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13170262	0.82[ASN][1000 genomes]
rs13171497	0.80[ASN][1000 genomes]
rs13171757	0.88[ASN][1000 genomes]
rs13172080	0.82[ASN][1000 genomes]
rs13172084	0.80[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs13178686	1.00[ASN][1000 genomes]
rs13179091	0.80[ASN][1000 genomes]
rs13181015	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs13185068	0.80[ASN][1000 genomes]
rs13186194	0.80[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs13188327	0.93[ASN][1000 genomes]
rs13188685	0.80[ASN][1000 genomes]
rs1348716	0.82[ASN][1000 genomes]
rs1374043	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1445976	0.80[ASN][1000 genomes]
rs1445979	0.86[ASN][1000 genomes]
rs1445980	0.80[ASN][1000 genomes]
rs1445981	0.80[ASN][1000 genomes]
rs1477355	0.86[ASN][1000 genomes]
rs1986252	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2034239	0.80[ASN][1000 genomes]
rs2053693	0.80[ASN][1000 genomes]
rs2053694	0.80[ASN][1000 genomes]
rs2276987	0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs28610339	0.99[ASN][1000 genomes]
rs34739794	0.98[ASN][1000 genomes]
rs35262187	1.00[ASN][1000 genomes]
rs4132385	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4276369	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4352559	0.81[CEU][hapmap];0.80[MEX][hapmap]
rs4391122	0.85[CEU][hapmap];0.88[YRI][hapmap]
rs4392578	1.00[ASN][1000 genomes]
rs4484384	1.00[ASN][1000 genomes]
rs4546329	0.83[MEX][hapmap];0.80[TSI][hapmap]
rs4700418	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs5027472	0.91[ASN][1000 genomes]
rs55838118	0.80[ASN][1000 genomes]
rs56035042	1.00[ASN][1000 genomes]
rs60529601	1.00[ASN][1000 genomes]
rs60886975	1.00[ASN][1000 genomes]
rs62368660	1.00[ASN][1000 genomes]
rs6449528	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6449529	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6449530	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6449531	0.99[ASN][1000 genomes]
rs6449532	0.99[ASN][1000 genomes]
rs6449533	0.99[ASN][1000 genomes]
rs6449535	0.86[ASN][1000 genomes]
rs66775554	0.80[ASN][1000 genomes]
rs6860608	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6865624	0.80[ASN][1000 genomes]
rs6873712	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs6874264	0.80[ASN][1000 genomes]
rs6877610	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6878927	0.80[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap]
rs6879809	0.85[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs6881765	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6885005	0.99[ASN][1000 genomes]
rs6890351	0.80[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs6890684	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6894675	0.99[ASN][1000 genomes]
rs6895046	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7443602	0.80[ASN][1000 genomes]
rs7700289	1.00[ASN][1000 genomes]
rs7701440	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7709645	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7714457	0.82[ASN][1000 genomes]
rs7714712	0.99[ASN][1000 genomes]
rs7717082	0.82[ASN][1000 genomes]
rs7719647	0.82[ASN][1000 genomes]
rs7720894	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7722810	0.87[ASN][1000 genomes]
rs7724551	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7727824	0.99[ASN][1000 genomes]
rs7732234	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7734879	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv823089	chr5:60589501-60669903	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv1815974	chr5:60626344-60664356	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60631000-60644000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr5:60631400-60652800	Weak transcription	Primary B cells from cord blood	blood
3	chr5:60632000-60648600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:60633600-60643200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr5:60636200-60644400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:60637200-60643200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr5:60637200-60644000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr5:60637200-60645800	Weak transcription	Stomach Mucosa	stomach
9	chr5:60637200-60647600	Weak transcription	Colonic Mucosa	Colon
10	chr5:60637200-60651200	Enhancers	Brain Anterior Caudate	brain
11	chr5:60638000-60643000	Weak transcription	Spleen	Spleen
12	chr5:60638000-60643200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr5:60638000-60651200	Enhancers	Brain Hippocampus Middle	brain
14	chr5:60638200-60643000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr5:60638200-60653000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr5:60638400-60646000	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr5:60638400-60648600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr5:60638400-60650600	Enhancers	Brain Substantia Nigra	brain
19	chr5:60638400-60653000	Weak transcription	NHEK	skin
20	chr5:60638400-60655000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr5:60638400-60665200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr5:60638600-60642800	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr5:60638800-60650600	Enhancers	Brain Angular Gyrus	brain
24	chr5:60639200-60643400	Enhancers	Liver	Liver
25	chr5:60640000-60643400	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr5:60640400-60642800	Weak transcription	NHDF-Ad	bronchial
27	chr5:60640400-60647800	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr5:60640400-60652800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr5:60640400-60665600	Weak transcription	Gastric	stomach
30	chr5:60640600-60643000	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr5:60640600-60643000	Weak transcription	Esophagus	oesophagus
32	chr5:60640600-60643000	Weak transcription	Left Ventricle	heart
33	chr5:60640600-60643000	Weak transcription	Lung	lung
34	chr5:60640600-60643000	Weak transcription	Ovary	ovary
35	chr5:60640600-60643000	Weak transcription	Psoas Muscle	Psoas
36	chr5:60640600-60643000	Weak transcription	Right Atrium	heart
37	chr5:60640600-60643000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr5:60640600-60643200	Weak transcription	Primary B cells from peripheral blood	blood
39	chr5:60640600-60644200	Weak transcription	Fetal Intestine Large	intestine
40	chr5:60640600-60644600	Weak transcription	Duodenum Mucosa	Duodenum
41	chr5:60640600-60645800	Weak transcription	Right Ventricle	heart
42	chr5:60640600-60647800	Weak transcription	Aorta	Aorta
43	chr5:60640600-60648600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr5:60640600-60658400	Weak transcription	Fetal Brain Female	brain
45	chr5:60640600-60658400	Weak transcription	NHLF	lung
46	chr5:60640800-60642800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr5:60640800-60643000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr5:60640800-60643000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr5:60640800-60643000	Weak transcription	Pancreas	Pancrea
50	chr5:60640800-60643200	Weak transcription	Stomach Smooth Muscle	stomach

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