Variant report

Variant	rs7314170
Chromosome Location	chr12:21579080-21579081
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:21578861..21581322-chr12:21589967..21591700,2	MCF-7	breast:
2	chr12:21570524..21573513-chr12:21578970..21581790,2	K562	blood:
3	chr12:21578534..21580531-chr12:21589180..21591050,2	K562	blood:

Variant related genes	Relation type
ENSG00000121350	Chromatin interaction
ENSG00000084453	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10161011	0.90[ASN][1000 genomes]
rs10161132	0.82[CHB][hapmap]
rs10437776	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs10770808	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs10770810	0.86[CHB][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10770814	0.87[ASN][1000 genomes]
rs10770815	0.87[ASN][1000 genomes]
rs10841808	0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs10841809	0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10841810	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10841815	0.82[CHB][hapmap]
rs10841821	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10841822	0.83[ASN][1000 genomes]
rs11046050	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs11046055	0.82[CHB][hapmap]
rs11046064	0.82[CHB][hapmap]
rs11046065	0.80[CHB][hapmap]
rs11046070	0.87[ASN][1000 genomes]
rs11046071	0.87[ASN][1000 genomes]
rs11046073	0.87[ASN][1000 genomes]
rs11608682	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs11610942	0.82[CHB][hapmap];0.83[MEX][hapmap];0.85[AMR][1000 genomes]
rs12228018	0.85[AMR][1000 genomes]
rs12372774	0.82[CHB][hapmap];0.85[AMR][1000 genomes]
rs12423128	0.87[ASN][1000 genomes]
rs12423151	0.84[ASN][1000 genomes]
rs13035	0.86[AMR][1000 genomes]
rs1476904	0.81[CHB][hapmap]
rs1476905	0.82[CHB][hapmap]
rs1476907	0.82[CHB][hapmap]
rs1860949	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs1963330	0.87[ASN][1000 genomes]
rs1963817	0.86[CHB][hapmap];0.81[CHD][hapmap];0.83[MEX][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2058463	0.82[CHB][hapmap]
rs2058464	0.82[CHB][hapmap]
rs2110165	0.82[CHB][hapmap]
rs2159947	0.87[ASN][1000 genomes]
rs2159948	0.82[CHB][hapmap]
rs2192179	0.87[ASN][1000 genomes]
rs2192182	0.86[ASN][1000 genomes]
rs2192183	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs2215734	0.82[CHB][hapmap]
rs2302499	0.87[ASN][1000 genomes]
rs2302500	0.86[CHB][hapmap];0.81[CHD][hapmap];0.87[ASN][1000 genomes]
rs2417979	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs2417980	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs2417981	0.86[CHB][hapmap];0.81[CHD][hapmap];0.87[ASN][1000 genomes]
rs2417982	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs2417983	0.87[ASN][1000 genomes]
rs2417984	0.82[CHB][hapmap]
rs28690452	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3213210	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3213211	0.87[ASN][1000 genomes]
rs3752648	0.82[CHB][hapmap]
rs3759229	0.82[CHB][hapmap]
rs3782660	0.86[CHB][hapmap];0.81[CHD][hapmap];0.87[ASN][1000 genomes]
rs3825287	0.81[CHB][hapmap]
rs3825289	0.87[ASN][1000 genomes]
rs4388943	0.87[ASN][1000 genomes]
rs4388944	0.87[ASN][1000 genomes]
rs4423237	0.87[ASN][1000 genomes]
rs4491287	0.84[ASN][1000 genomes]
rs4551820	0.87[ASN][1000 genomes]
rs4762829	0.82[CHB][hapmap]
rs4762830	0.82[CHB][hapmap]
rs4762831	0.82[CHB][hapmap]
rs61926294	0.87[ASN][1000 genomes]
rs61926296	0.84[ASN][1000 genomes]
rs6487222	0.82[CHB][hapmap]
rs6487223	0.82[CHB][hapmap]
rs6487224	0.87[ASN][1000 genomes]
rs6487226	0.87[ASN][1000 genomes]
rs6487227	0.87[ASN][1000 genomes]
rs6487229	0.82[CHB][hapmap]
rs6487230	0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs6487231	0.86[ASN][1000 genomes]
rs7131777	0.87[ASN][1000 genomes]
rs7133827	0.87[ASN][1000 genomes]
rs7134243	0.82[CHB][hapmap]
rs7135390	0.82[CHB][hapmap];0.83[MEX][hapmap];0.83[AMR][1000 genomes]
rs7136175	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs7136257	0.86[CHB][hapmap];0.81[CHD][hapmap];0.87[ASN][1000 genomes]
rs7136265	0.86[CHB][hapmap];0.81[CHD][hapmap];0.87[ASN][1000 genomes]
rs7137034	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs7138359	0.87[ASN][1000 genomes]
rs714356	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs714357	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs7294351	0.87[ASN][1000 genomes]
rs7295417	0.87[ASN][1000 genomes]
rs7295570	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs7296273	0.87[ASN][1000 genomes]
rs7297084	0.86[ASN][1000 genomes]
rs7303408	0.82[CHB][hapmap]
rs7308263	0.87[ASN][1000 genomes]
rs7309539	0.87[ASN][1000 genomes]
rs7310953	0.82[CHB][hapmap]
rs738028	0.86[CHB][hapmap];0.81[CHD][hapmap];0.87[ASN][1000 genomes]
rs7964568	0.87[ASN][1000 genomes]
rs7970416	0.86[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7971031	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7980957	0.87[ASN][1000 genomes]
rs917855	0.82[CHB][hapmap]
rs9788091	0.83[CHD][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap]
rs997820	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519603	chr12:21526472-21584709	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv898894	chr12:21545532-21583242	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv526789	chr12:21555691-21590788	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
4	nsv898895	chr12:21561645-21621891	Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
5	nsv898896	chr12:21561645-21695584	Strong transcription Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv1043936	chr12:21562673-21979030	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv557741	chr12:21578559-22169854	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv469163	chr12:21579080-21592357	Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
9	nsv557742	chr12:21579080-21592357	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7314170	PYROXD1	cis	lymphoblastoid	seeQTL
rs7314170	PYROXD1	Cis_1M	lymphoblastoid	RTeQTL
rs7314170	PYROXD1	cis	cerebellum	SCAN
rs7314170	PYROXD1	cis	parietal	SCAN
rs7314170	RECQL	cis	cerebellum	SCAN
rs7314170	LOC642732	Cis_1M	lymphoblastoid	RTeQTL
rs7314170	RECQL	Cis_1M	lymphoblastoid	RTeQTL
rs7314170	LOC642732///PYROXD1	Cis_1M	lymphoblastoid	RTeQTL

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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