Variant report

Variant	rs4649996
Chromosome Location	chr1:74520279-74520280
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1032082	0.81[CEU][hapmap];0.82[JPT][hapmap]
rs10493530	0.83[CEU][hapmap]
rs10493531	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10789387	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs10789388	0.83[CEU][hapmap];0.83[JPT][hapmap]
rs10890108	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11210404	0.83[CEU][hapmap];0.83[JPT][hapmap]
rs11210405	0.80[JPT][hapmap]
rs11210417	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11210418	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[YRI][hapmap]
rs11210419	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs11579809	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11806946	0.96[CEU][hapmap];0.93[YRI][hapmap]
rs1412825	0.96[CEU][hapmap];0.94[YRI][hapmap]
rs1483793	0.96[CEU][hapmap];0.83[CHB][hapmap];0.94[YRI][hapmap]
rs1483795	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs1601153	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs1843023	0.83[CEU][hapmap];0.83[JPT][hapmap]
rs2128935	0.83[JPT][hapmap]
rs2343864	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[YRI][hapmap]
rs3765651	0.93[YRI][hapmap]
rs4142948	0.83[CEU][hapmap];0.83[JPT][hapmap]
rs4142949	0.82[JPT][hapmap]
rs4422957	0.96[CEU][hapmap];0.93[YRI][hapmap]
rs4650243	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4650245	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs481387	0.93[YRI][hapmap]
rs487917	0.96[CEU][hapmap];0.94[YRI][hapmap]
rs489941	0.92[CEU][hapmap];0.80[YRI][hapmap]
rs495027	0.96[CEU][hapmap];0.94[YRI][hapmap]
rs500203	0.87[YRI][hapmap]
rs520806	0.96[CEU][hapmap];0.93[YRI][hapmap]
rs522759	0.96[CEU][hapmap];0.94[YRI][hapmap]
rs524306	0.95[CEU][hapmap];0.81[CHB][hapmap]
rs545664	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs545721	0.96[CEU][hapmap];0.93[YRI][hapmap]
rs568049	0.94[YRI][hapmap]
rs571848	0.96[CEU][hapmap];0.93[YRI][hapmap]
rs577367	0.96[CEU][hapmap];0.93[YRI][hapmap]
rs6676103	0.83[CEU][hapmap];0.83[JPT][hapmap]
rs6676622	0.82[CEU][hapmap];0.83[JPT][hapmap]
rs7535929	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs7543134	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs7550195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs792310	0.96[CEU][hapmap];0.93[YRI][hapmap]
rs792321	0.96[CEU][hapmap];0.93[YRI][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	nsv470717	chr1:74445584-74532587	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	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
10	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
11	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
12	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
13	nsv871527	chr1:74501477-74560002	Enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4649996	FPGT	cis	Muscle Skeletal	GTEx
rs4649996	LRRIQ3	cis	Thyroid	GTEx
rs4649996	LRRC44	Cis_1M	lymphoblastoid	RTeQTL
rs4649996	MGC22773	cis	multi-tissue	Pritchard
rs4649996	LRRIQ3	cis	Nerve Tibial	GTEx

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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