Variant report

Variant	rs7514705
Chromosome Location	chr1:75006720-75006721
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10218727	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1040070	0.96[CEU][hapmap];0.85[CHB][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10493544	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10789396	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10890130	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11210476	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11210477	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11210478	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12036473	0.86[CEU][hapmap]
rs12041852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12041912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12042908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12142020	0.92[CEU][hapmap]
rs12566985	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12568287	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1514173	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1514174	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1514175	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1514176	0.93[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1514177	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2344508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34062471	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3765680	0.93[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3765681	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3843262	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3845344	0.89[CEU][hapmap]
rs3845345	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3845347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3894212	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3895907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650277	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604866	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6604867	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604871	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6604872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6656785	0.89[CEU][hapmap]
rs6690871	0.96[CEU][hapmap]
rs6695685	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6698622	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6698760	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6703637	0.93[CEU][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7520945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7525548	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7526762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7551507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7553158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7553348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs953567	0.88[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003171	chr1:74407468-75122270	Strong transcription Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv535000	chr1:74407468-75122270	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv1011745	chr1:74730942-75477618	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv535003	chr1:74730942-75477618	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv830248	chr1:74962391-75144458	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1003356	chr1:74983681-75024938	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv871900	chr1:74983835-75014195	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv2752695	chr1:74995225-75008411	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv2755299	chr1:74995225-75008411	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv432387	chr1:74995225-75008411	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Menarche (age at onset)	25231870	GWAS catalog

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:74990200-75017200	Weak transcription	Left Ventricle	heart
2	chr1:75000800-75012400	Weak transcription	Fetal Heart	heart
3	chr1:75005800-75007000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:75006000-75007400	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr1:75006400-75006800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:75006400-75006800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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