Variant report

Variant	rs12318618
Chromosome Location	chr12:49713629-49713630
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49696884..49699864-chr12:49712241..49714234,3	K562	blood:
2	chr12:49663971..49666837-chr12:49712458..49715347,2	K562	blood:
3	chr12:49657378..49660291-chr12:49711061..49714254,5	K562	blood:
4	chr12:49657378..49660931-chr12:49711552..49714180,3	K562	blood:
5	chr12:49698201..49699864-chr12:49712717..49714234,2	K562	blood:
6	chr12:49686580..49692358-chr12:49712251..49718367,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135406	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000167553	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10400435	0.91[CEU][hapmap];0.82[MEX][hapmap]
rs10506284	1.00[CHB][hapmap]
rs10875946	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10875948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168967	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11168970	0.93[ASN][1000 genomes]
rs11168971	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168972	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168975	1.00[JPT][hapmap]
rs11169016	1.00[CHB][hapmap]
rs11169048	1.00[CHB][hapmap]
rs11830144	0.81[TSI][hapmap]
rs11834161	1.00[CHB][hapmap]
rs11835037	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11835303	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs11837234	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12301545	0.93[ASN][1000 genomes]
rs12301632	1.00[CHB][hapmap]
rs12304800	0.93[ASN][1000 genomes]
rs12305716	1.00[CHB][hapmap]
rs12306118	1.00[CHB][hapmap]
rs12310595	0.82[AMR][1000 genomes]
rs12313435	0.93[ASN][1000 genomes]
rs12315095	0.93[ASN][1000 genomes]
rs12315130	0.93[ASN][1000 genomes]
rs12315996	1.00[CHB][hapmap]
rs12317532	0.93[ASN][1000 genomes]
rs12322335	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12322497	0.84[AMR][1000 genomes]
rs12322506	0.84[AMR][1000 genomes]
rs12322561	1.00[CHB][hapmap]
rs12322798	0.93[ASN][1000 genomes]
rs12580931	1.00[JPT][hapmap]
rs12581307	0.85[ASN][1000 genomes]
rs12581343	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs12581428	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12582651	0.82[AMR][1000 genomes]
rs12582901	0.82[AMR][1000 genomes]
rs12822293	1.00[CEU][hapmap];0.87[GIH][hapmap];0.80[MEX][hapmap]
rs2070761	0.93[ASN][1000 genomes]
rs2230550	1.00[ASN][1000 genomes]
rs2236746	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2272478	1.00[CHB][hapmap]
rs28543370	0.93[ASN][1000 genomes]
rs28798494	0.93[ASN][1000 genomes]
rs28823960	0.93[ASN][1000 genomes]
rs28857010	0.93[ASN][1000 genomes]
rs3088008	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap]
rs34791911	0.93[ASN][1000 genomes]
rs3847764	1.00[CHB][hapmap];0.84[AMR][1000 genomes]
rs3898446	0.93[ASN][1000 genomes]
rs4243545	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs4382953	0.83[CEU][hapmap];0.82[AMR][1000 genomes]
rs4898502	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs4898504	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4898516	0.93[ASN][1000 genomes]
rs4898517	0.93[ASN][1000 genomes]
rs4898519	0.91[CEU][hapmap];1.00[JPT][hapmap]
rs56911877	0.84[EUR][1000 genomes]
rs57451017	0.93[ASN][1000 genomes]
rs57755392	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59990555	0.84[EUR][1000 genomes]
rs60174686	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61023481	0.93[ASN][1000 genomes]
rs61455481	0.93[ASN][1000 genomes]
rs61649357	0.88[EUR][1000 genomes]
rs6580707	1.00[CHB][hapmap]
rs6580709	1.00[CHB][hapmap]
rs6580716	1.00[CHB][hapmap]
rs7136538	0.93[ASN][1000 genomes]
rs7136945	0.93[ASN][1000 genomes]
rs7139061	1.00[CHB][hapmap]
rs7294648	1.00[CHB][hapmap]
rs7294873	0.93[ASN][1000 genomes]
rs7294973	1.00[CHB][hapmap]
rs7295162	1.00[CHB][hapmap]
rs7295247	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7309997	1.00[CHB][hapmap]
rs73309973	0.87[EUR][1000 genomes]
rs7342318	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7342365	1.00[CHB][hapmap]
rs7342370	0.93[ASN][1000 genomes]
rs7342384	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7397166	0.86[EUR][1000 genomes]
rs7398252	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7955541	1.00[CHB][hapmap]
rs7962951	1.00[CHB][hapmap]
rs7969099	1.00[CHB][hapmap]
rs7975431	0.93[ASN][1000 genomes]
rs7976165	1.00[CHB][hapmap]
rs9919740	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
5	nsv1042122	chr12:49678529-49823168	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
6	nsv1039176	chr12:49678529-49832618	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12318618	PRPH	cis	cerebellum	SCAN
rs12318618	TMEM117	cis	cerebellum	SCAN
rs12318618	DDN	cis	parietal	SCAN
rs12318618	C1QL4	cis	Thyroid	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49703800-49715600	Weak transcription	K562	blood
2	chr12:49709600-49715800	Weak transcription	NHEK	skin
3	chr12:49709600-49716000	Weak transcription	Fetal Intestine Small	intestine
4	chr12:49709800-49716000	Weak transcription	HMEC	breast

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