Variant report

Variant	rs6680736
Chromosome Location	chr1:62749872-62749873
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10493318	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs10889316	0.95[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs11207950	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs11207955	0.81[CEU][hapmap]
rs11207956	0.89[EUR][1000 genomes]
rs11579934	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs11584786	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs12031176	0.83[CEU][hapmap]
rs12123763	0.89[EUR][1000 genomes]
rs12127630	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs12127930	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs12138544	0.83[EUR][1000 genomes]
rs1325738	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[MEX][hapmap];0.91[ASN][1000 genomes]
rs1886830	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs1925825	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[ASN][1000 genomes]
rs2666467	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2765254	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2765255	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.87[MKK][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2765260	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2765262	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs34477066	0.87[EUR][1000 genomes]
rs3850632	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs3850633	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3903928	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4915810	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6691591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9803815	0.81[CEU][hapmap]
rs9804022	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1009398	chr1:62656660-62780644	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1013582	chr1:62723703-62910632	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62734200-62750800	Weak transcription	Gastric	stomach
2	chr1:62738200-62751200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr1:62744800-62750800	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr1:62747200-62751600	Weak transcription	Liver	Liver
5	chr1:62747400-62750600	Weak transcription	Pancreas	Pancrea
6	chr1:62747600-62751400	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr1:62748000-62751800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr1:62748400-62750400	Enhancers	Fetal Muscle Trunk	muscle
9	chr1:62748400-62750800	Weak transcription	HMEC	breast
10	chr1:62748400-62752400	Enhancers	Fetal Muscle Leg	muscle
11	chr1:62748600-62750000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:62748800-62750000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:62748800-62751000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:62748800-62751600	Enhancers	Fetal Stomach	stomach
15	chr1:62749000-62750000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
16	chr1:62749000-62750000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
17	chr1:62749000-62750000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:62749000-62750200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:62749000-62750400	Enhancers	Fetal Kidney	kidney
20	chr1:62749000-62751600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:62749000-62751600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:62749000-62751800	Enhancers	HepG2	liver
23	chr1:62749000-62753000	Enhancers	Fetal Lung	lung
24	chr1:62749200-62750000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
25	chr1:62749200-62750000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
26	chr1:62749200-62750200	Enhancers	Primary hematopoietic stem cells	blood
27	chr1:62749200-62750200	Enhancers	Adipose Nuclei	Adipose
28	chr1:62749400-62751000	Weak transcription	Brain Anterior Caudate	brain
29	chr1:62749400-62751600	Weak transcription	Placenta	Placenta
30	chr1:62749400-62751800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:62749600-62750000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr1:62749600-62751600	Weak transcription	Fetal Heart	heart

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