Variant report

Variant	rs6709090
Chromosome Location	chr2:179923685-179923686
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 102 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10497530	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10497531	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10497532	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11883598	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11883599	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11883748	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11885227	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11885400	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11885450	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11886627	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11887988	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11888041	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11890988	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11891599	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11891608	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11891654	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11892227	0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11893153	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11893315	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11895391	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11896002	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11896686	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11897059	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11899563	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11901386	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11901918	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11902355	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11903793	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12467652	0.96[EUR][1000 genomes]
rs12474600	0.93[EUR][1000 genomes]
rs12622222	0.80[CEU][hapmap]
rs16866624	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17362972	0.93[EUR][1000 genomes]
rs17363006	0.97[EUR][1000 genomes]
rs17363057	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17453612	1.00[CHD][hapmap]
rs17454087	0.80[CEU][hapmap]
rs17454199	0.80[CEU][hapmap]
rs1875779	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1875782	0.93[EUR][1000 genomes]
rs34190485	0.84[EUR][1000 genomes]
rs35465824	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35888089	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35901501	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35979436	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36098953	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4435492	0.93[EUR][1000 genomes]
rs4893864	0.92[EUR][1000 genomes]
rs4991006	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61397643	0.96[EUR][1000 genomes]
rs62175366	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62175367	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62175401	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62175402	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62175403	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62175411	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62175413	0.86[ASN][1000 genomes]
rs62175419	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62175420	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62175421	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62175422	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62175444	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62175990	0.93[EUR][1000 genomes]
rs62175993	0.93[EUR][1000 genomes]
rs62175994	0.93[EUR][1000 genomes]
rs62175995	0.93[EUR][1000 genomes]
rs62176021	0.93[EUR][1000 genomes]
rs62176023	0.97[EUR][1000 genomes]
rs62176024	0.97[EUR][1000 genomes]
rs62176026	0.97[EUR][1000 genomes]
rs62176027	0.97[EUR][1000 genomes]
rs62176028	0.97[EUR][1000 genomes]
rs6433747	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433748	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433749	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433750	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433751	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433752	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6712648	0.82[AFR][1000 genomes]
rs6716599	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6716713	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6716728	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6731564	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6731566	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6734597	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7574853	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7575047	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7578521	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7578961	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7579263	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7582862	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7588765	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7596842	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7601179	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7605060	0.86[ASN][1000 genomes]
rs7609150	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949133	chr2:179711376-180124327	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv875457	chr2:179775893-179966804	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv875458	chr2:179780624-179966804	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv875464	chr2:179843612-179939493	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv875465	chr2:179843612-179966804	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv508184	chr2:179896384-179965419	Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179921800-179924400	Enhancers	HUES6 Cell Line	embryonic stem cell
2	chr2:179922000-179924200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:179922200-179924000	Enhancers	HSMM	muscle
4	chr2:179922200-179924600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr2:179922400-179924600	Enhancers	Fetal Heart	heart
6	chr2:179922600-179924400	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr2:179922600-179924400	Enhancers	Primary B cells from peripheral blood	blood
8	chr2:179922600-179924800	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr2:179922800-179923800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
10	chr2:179922800-179924000	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr2:179922800-179924000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:179922800-179924200	Enhancers	Adipose Nuclei	Adipose
13	chr2:179922800-179924400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:179922800-179924600	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr2:179922800-179924800	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr2:179922800-179925200	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr2:179923000-179923800	Enhancers	Muscle Satellite Cultured Cells	--
18	chr2:179923200-179923800	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr2:179923200-179923800	Enhancers	Brain Substantia Nigra	brain
20	chr2:179923200-179924200	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr2:179923200-179924600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:179923200-179924600	Enhancers	HSMMtube	muscle
23	chr2:179923200-179924800	Enhancers	Primary B cells from cord blood	blood
24	chr2:179923400-179923800	Flanking Active TSS	GM12878-XiMat	blood
25	chr2:179923400-179924000	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr2:179923400-179924200	Enhancers	Fetal Kidney	kidney
27	chr2:179923400-179924800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr2:179923600-179924600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr2:179923600-179933800	Weak transcription	Gastric	stomach

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