Variant report

Variant	rs1483795
Chromosome Location	chr1:74542927-74542928
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1032082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap]
rs10493529	0.80[CHD][hapmap]
rs10493530	1.00[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap]
rs10493531	0.82[JPT][hapmap]
rs10789387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap]
rs10789388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10890108	0.82[JPT][hapmap]
rs11210404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11210405	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs11210407	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs11210417	0.82[CEU][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11210418	0.82[CEU][hapmap];0.82[YRI][hapmap]
rs11210427	0.86[CHB][hapmap]
rs11579809	0.82[JPT][hapmap]
rs11806946	0.87[ASW][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap]
rs12029606	0.86[CHB][hapmap]
rs12029814	0.84[CHB][hapmap]
rs12036659	0.86[CHB][hapmap]
rs12043976	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs12046751	0.86[CHB][hapmap]
rs12048351	0.86[CHB][hapmap];0.85[CHD][hapmap]
rs12122433	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs12402231	0.86[CHB][hapmap]
rs12410230	0.86[CHB][hapmap]
rs12746942	0.86[CHB][hapmap]
rs12746996	0.86[CHB][hapmap]
rs1412825	0.81[CEU][hapmap];0.82[YRI][hapmap]
rs1483793	0.82[YRI][hapmap]
rs1601153	0.82[CEU][hapmap];0.91[TSI][hapmap]
rs17524893	0.86[CHB][hapmap];0.80[CHD][hapmap];0.85[ASN][1000 genomes]
rs1843023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs1856789	0.86[CHB][hapmap]
rs1930588	0.86[CHB][hapmap]
rs2035473	0.86[CHB][hapmap]
rs2128935	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2343864	0.82[CEU][hapmap];0.82[YRI][hapmap]
rs3765651	0.87[ASW][hapmap];0.91[LWK][hapmap];0.98[MKK][hapmap];0.82[YRI][hapmap]
rs4142948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs4142949	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs4422957	0.87[ASW][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap]
rs4649996	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs4650243	0.82[JPT][hapmap]
rs4650245	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap]
rs481387	0.87[ASW][hapmap];0.91[LWK][hapmap];0.98[MKK][hapmap];0.82[YRI][hapmap]
rs487917	0.82[YRI][hapmap]
rs489941	0.87[ASW][hapmap];0.91[LWK][hapmap];0.97[MKK][hapmap];0.82[TSI][hapmap]
rs495027	0.81[YRI][hapmap]
rs520806	0.87[ASW][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap]
rs522759	0.82[YRI][hapmap]
rs524306	0.85[YRI][hapmap]
rs545664	0.84[CEU][hapmap];0.87[YRI][hapmap]
rs545721	0.81[YRI][hapmap]
rs568049	0.82[YRI][hapmap]
rs571848	0.87[ASW][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap]
rs577367	0.95[LWK][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap]
rs6676103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6676622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6680375	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7529384	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs7535929	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap]
rs7550195	0.81[CEU][hapmap];0.82[JPT][hapmap];0.82[YRI][hapmap]
rs792310	0.87[ASW][hapmap];0.95[MKK][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap]
rs792321	0.87[ASW][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap]
rs9804006	0.86[CHB][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	nsv1004451	chr1:74107125-74874389	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv534999	chr1:74107125-74874389	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv522147	chr1:74338530-74983835	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv1013244	chr1:74441655-74680703	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv535001	chr1:74441655-74680703	Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv871269	chr1:74484753-74709362	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
9	nsv871381	chr1:74484753-74712181	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
10	nsv871084	chr1:74492200-74681968	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
11	nsv871456	chr1:74492200-74712181	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
12	nsv871527	chr1:74501477-74560002	Enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv1008285	chr1:74517953-74705457	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
14	nsv947274	chr1:74537777-74546267	Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1483795	TNNI3K	cis	cerebellum	SCAN
rs1483795	LRRC44	Cis_1M	lymphoblastoid	RTeQTL
rs1483795	LRRIQ3	cis	Nerve Tibial	GTEx
rs1483795	MGC22773	cis	multi-tissue	Pritchard
rs1483795	ASB17	cis	parietal	SCAN
rs1483795	LRRIQ3	cis	Thyroid	GTEx
rs1483795	FPGT	cis	Muscle Skeletal	GTEx
rs1483795	FPGT	cis	cerebellum	SCAN
rs1483795	LRRIQ3	cis	parietal	SCAN
rs1483795	FPGT	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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