Variant report

Variant	rs740341
Chromosome Location	chr7:110497173-110497174
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12536318	0.89[CEU][hapmap];0.84[MEX][hapmap];0.83[EUR][1000 genomes]
rs12705741	0.83[EUR][1000 genomes]
rs1406049	0.82[EUR][1000 genomes]
rs1859846	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2190527	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2190528	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2190529	0.83[EUR][1000 genomes]
rs2396282	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs258975	0.96[CEU][hapmap];0.86[CHB][hapmap]
rs258978	0.96[CEU][hapmap];0.85[CHB][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs258979	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs258982	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs258983	0.96[CEU][hapmap];0.86[CHB][hapmap]
rs258984	0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap]
rs258998	0.82[CEU][hapmap]
rs6466363	0.80[MEX][hapmap]
rs6944312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6948090	0.80[MEX][hapmap]
rs6973561	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs764864	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs799616	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs799618	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs799620	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs799623	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.88[LWK][hapmap];0.87[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs799624	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.88[LWK][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs799625	1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs799626	0.83[EUR][1000 genomes]
rs799628	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs799642	0.86[EUR][1000 genomes]
rs799643	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs9656177	0.85[CEU][hapmap]
rs9886295	0.89[CEU][hapmap];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016758	chr7:109834827-110549197	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv539059	chr7:109834827-110549197	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1023596	chr7:109984459-110708071	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv539061	chr7:109984459-110708071	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv1032498	chr7:110151471-110508283	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv608147	chr7:110292046-110617845	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv531434	chr7:110310931-110839892	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv888972	chr7:110470629-110635497	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	esv3506497	chr7:110484691-111091738	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	esv3506498	chr7:110484750-111091689	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv608152	chr7:110488367-110520903	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv608153	chr7:110488367-110534002	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs740341	THAP5	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:110496400-110497200	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr7:110496400-110498000	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr7:110496400-110498600	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr7:110496600-110497200	Enhancers	H1 Cell Line	embryonic stem cell
5	chr7:110496600-110497400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr7:110496600-110497600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr7:110496600-110498000	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr7:110496600-110498200	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr7:110496800-110497200	Enhancers	H9 Cell Line	embryonic stem cell
10	chr7:110496800-110497200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:110496800-110497200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr7:110496800-110497200	Enhancers	Ovary	ovary
13	chr7:110496800-110497400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr7:110496800-110498000	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr7:110497000-110497200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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