Variant report

Variant	rs1417391
Chromosome Location	chr6:54071413-54071414
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1028804	0.81[CEU][hapmap];0.84[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1093331	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10948798	0.83[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10948803	0.90[CHB][hapmap]
rs1150875	0.87[JPT][hapmap]
rs1150884	0.81[JPT][hapmap]
rs1150887	0.80[ASN][1000 genomes]
rs11757700	0.90[CHB][hapmap];0.80[LWK][hapmap];0.85[MEX][hapmap]
rs1280946	0.82[CEU][hapmap];0.84[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1280949	0.82[CEU][hapmap];0.84[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1299293	0.81[JPT][hapmap]
rs1321886	0.86[YRI][hapmap]
rs1321892	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs1340667	0.81[JPT][hapmap]
rs1407229	0.84[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1407231	0.87[EUR][1000 genomes]
rs1407232	0.86[CEU][hapmap];0.90[YRI][hapmap];0.87[EUR][1000 genomes]
rs1407235	0.85[CEU][hapmap];0.86[YRI][hapmap];0.87[EUR][1000 genomes]
rs1407236	0.86[CEU][hapmap];0.90[YRI][hapmap];0.87[EUR][1000 genomes]
rs1407237	0.85[CEU][hapmap];0.89[YRI][hapmap];0.87[EUR][1000 genomes]
rs1417389	0.90[CHB][hapmap];0.82[YRI][hapmap]
rs16884761	0.87[JPT][hapmap]
rs16884943	0.81[JPT][hapmap]
rs16884946	0.81[JPT][hapmap]
rs1830949	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs2145754	0.81[CEU][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes]
rs2145755	0.87[EUR][1000 genomes]
rs2145759	0.87[EUR][1000 genomes]
rs2145761	0.81[JPT][hapmap]
rs2180931	0.90[CHB][hapmap]
rs2185505	0.90[CHB][hapmap]
rs2754795	0.81[JPT][hapmap]
rs2754798	0.81[JPT][hapmap]
rs2754809	0.86[CEU][hapmap]
rs2792634	0.81[JPT][hapmap]
rs2797425	0.86[CEU][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.87[LWK][hapmap];0.86[YRI][hapmap];0.87[EUR][1000 genomes]
rs34961553	0.80[AFR][1000 genomes]
rs3903931	0.82[CEU][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes]
rs4301306	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs4521576	0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs4712056	0.82[CEU][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes]
rs4712059	0.90[CHB][hapmap]
rs486135	0.82[CEU][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs490628	0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs506096	0.81[CEU][hapmap];0.83[JPT][hapmap];0.81[EUR][1000 genomes]
rs515501	0.81[CEU][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs519978	0.82[CEU][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs521584	0.85[EUR][1000 genomes]
rs524332	0.85[EUR][1000 genomes]
rs545829	0.82[CEU][hapmap];0.83[JPT][hapmap]
rs557224	0.85[EUR][1000 genomes]
rs581120	0.85[EUR][1000 genomes]
rs589208	0.84[EUR][1000 genomes]
rs600522	0.81[CEU][hapmap];0.83[JPT][hapmap];0.84[EUR][1000 genomes]
rs616579	0.82[CEU][hapmap];0.84[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs634042	0.82[CEU][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes]
rs6458988	0.85[CHB][hapmap]
rs665640	0.82[CEU][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes]
rs666104	0.85[EUR][1000 genomes]
rs667854	0.82[CEU][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes]
rs670463	0.82[CEU][hapmap];0.84[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs684940	0.83[JPT][hapmap]
rs685893	0.82[CEU][hapmap];0.83[JPT][hapmap]
rs6932559	0.89[CHB][hapmap]
rs6934690	0.81[JPT][hapmap]
rs6937413	0.89[CHB][hapmap]
rs7751241	0.81[JPT][hapmap]
rs816364	0.82[CEU][hapmap];0.84[CHB][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs816365	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs816367	0.82[CEU][hapmap];0.84[CHB][hapmap];0.83[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs816373	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs816375	0.87[EUR][1000 genomes]
rs816378	0.85[EUR][1000 genomes]
rs816379	0.86[CEU][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.81[LWK][hapmap];0.86[EUR][1000 genomes]
rs816382	0.90[CHB][hapmap]
rs816383	0.90[CHB][hapmap]
rs816385	0.90[CHB][hapmap]
rs816387	0.86[CEU][hapmap];0.84[CHB][hapmap];0.80[GIH][hapmap];0.83[JPT][hapmap];0.93[LWK][hapmap];0.83[MKK][hapmap];0.81[TSI][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs843826	0.81[CEU][hapmap]
rs864642	0.86[CEU][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.87[LWK][hapmap];0.90[YRI][hapmap];0.87[EUR][1000 genomes]
rs9296739	0.86[CEU][hapmap];0.84[CHB][hapmap];0.83[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9296740	0.84[CHB][hapmap]
rs9395908	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs9395916	0.90[CHB][hapmap]
rs9395917	0.90[CHB][hapmap]
rs9474746	0.80[JPT][hapmap]
rs9474754	0.81[JPT][hapmap]

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	nsv1067663	chr6:53796341-54449718	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv529158	chr6:53796341-54449718	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv603110	chr6:53885918-54103794	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1017633	chr6:53935336-54118476	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1417391	TINAG	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53998000-54099200	Weak transcription	Psoas Muscle	Psoas
2	chr6:54058800-54101000	Weak transcription	Left Ventricle	heart
3	chr6:54069200-54072000	Enhancers	HepG2	liver
4	chr6:54070200-54098800	Weak transcription	Fetal Heart	heart
5	chr6:54070400-54095200	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr6:54070600-54071600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr6:54071200-54071600	Enhancers	Muscle Satellite Cultured Cells	--
8	chr6:54071200-54071600	Enhancers	Hela-S3	cervix

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