Variant report

Variant	rs868824
Chromosome Location	chr7:110391921-110391922
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:110390258..110392332-chr7:110412106..110414900,2	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1013938	0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10500000	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10953667	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11762006	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11764173	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs11764228	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs11768241	0.84[CEU][hapmap];0.87[JPT][hapmap]
rs11982142	0.95[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs1528034	0.88[MEX][hapmap]
rs1540855	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1540856	0.92[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17157942	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17400357	0.83[MEX][hapmap]
rs1881164	1.00[ASW][hapmap];0.96[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs2008109	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2008117	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2030967	0.85[JPT][hapmap]
rs2191925	1.00[YRI][hapmap]
rs2396275	1.00[CEU][hapmap]
rs34856804	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34896727	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35403926	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4142915	0.91[CEU][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67082610	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6944830	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6954311	0.85[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6980230	0.88[CEU][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs7778910	0.89[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.86[ASN][1000 genomes]
rs7779870	0.88[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs7782454	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7803158	0.84[ASW][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap]
rs7803318	0.85[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9641446	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv1028635	chr7:109896582-110417137	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv539060	chr7:109896582-110417137	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	nsv539062	chr7:110185012-110392264	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1016284	chr7:110285283-110443365	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	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
11	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
12	nsv464673	chr7:110318027-110454356	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv608150	chr7:110318027-110454356	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	nsv608151	chr7:110391589-110439111	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs868824	TMEM168	cis	parietal	SCAN
rs868824	C7orf60	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:110388800-110402200	Weak transcription	Psoas Muscle	Psoas
2	chr7:110391400-110399000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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