Variant report

Variant	rs6668653
Chromosome Location	chr1:97608447-97608448
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10783055	0.81[AMR][1000 genomes]
rs10875049	0.85[ASW][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10875050	0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10875051	0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10875052	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10875053	0.84[ASW][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11165791	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11165792	0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11165793	0.85[ASW][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11165794	0.85[ASW][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11165795	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11165798	0.88[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.84[ASN][1000 genomes]
rs11165800	0.85[ASW][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11165803	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11165804	0.88[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11165805	0.88[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12029380	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12035468	0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12041436	0.88[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12091136	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12120077	0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12122422	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12124552	0.85[ASW][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12133566	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12134860	0.85[ASW][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12740796	0.88[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12759852	0.85[ASW][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1760209	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1760210	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17702702	0.86[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2991263	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs34031151	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4309030	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4390222	0.85[ASW][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.81[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6593633	0.82[ASN][1000 genomes]
rs7520102	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8179310	0.88[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes]
rs828053	0.85[ASW][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs828057	0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs828059	0.85[ASW][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs864341	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs993714	0.85[ASW][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][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	nsv491816	chr1:97266403-98223619	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv530048	chr1:97457175-98031501	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1007950	chr1:97466488-98021146	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv830692	chr1:97501492-97625153	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:97563600-97619200	Weak transcription	Dnd41	blood
2	chr1:97564200-97632800	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr1:97585600-97621800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr1:97592200-97608800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:97597400-97619600	Weak transcription	Liver	Liver
6	chr1:97603400-97610200	Weak transcription	Brain Germinal Matrix	brain
7	chr1:97604000-97610000	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr1:97604000-97620000	Weak transcription	Pancreas	Pancrea
9	chr1:97604200-97610400	Weak transcription	Fetal Brain Male	brain
10	chr1:97604400-97609200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:97604400-97609600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:97604400-97611000	Weak transcription	Stomach Mucosa	stomach
13	chr1:97604400-97614800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr1:97604400-97629000	Weak transcription	Primary B cells from cord blood	blood
15	chr1:97604600-97608800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:97604600-97608800	Weak transcription	Brain Anterior Caudate	brain
17	chr1:97604600-97609000	Weak transcription	Brain Hippocampus Middle	brain
18	chr1:97604600-97609000	Weak transcription	NHLF	lung
19	chr1:97604600-97609400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr1:97604600-97609400	Weak transcription	A549	lung
21	chr1:97604600-97609400	Weak transcription	HUVEC	blood vessel
22	chr1:97604600-97609600	Weak transcription	HSMMtube	muscle
23	chr1:97604600-97609800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:97604600-97609800	Weak transcription	Brain Angular Gyrus	brain
25	chr1:97604600-97610200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr1:97604600-97614000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:97604800-97609200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr1:97605200-97609000	Weak transcription	HSMM	muscle
29	chr1:97605400-97608800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:97605400-97608800	Weak transcription	NHDF-Ad	bronchial
31	chr1:97605400-97609000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:97605600-97608800	Weak transcription	Osteobl	bone
33	chr1:97605600-97609000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:97605800-97608600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr1:97606200-97610200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr1:97606200-97626600	Weak transcription	Ovary	ovary
37	chr1:97606800-97610400	Weak transcription	Primary T cells from cord blood	blood
38	chr1:97606800-97610400	Weak transcription	Aorta	Aorta
39	chr1:97607200-97611000	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr1:97607400-97608800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:97607400-97612600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:97608000-97608600	Weak transcription	Brain Substantia Nigra	brain
43	chr1:97608000-97609600	Enhancers	NH-A	brain
44	chr1:97608000-97610200	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr1:97608200-97609000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr1:97608200-97609400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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