Variant report

Variant	rs7170980
Chromosome Location	chr15:51956056-51956057
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:51955426..51957385-chr15:51970284..51973757,3	K562	blood:

Variant related genes	Relation type
ENSG00000104112	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10467923	0.81[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs10519313	0.80[CEU][hapmap];0.84[CHB][hapmap];0.95[TSI][hapmap]
rs1080394	0.81[CEU][hapmap]
rs11070857	0.81[CEU][hapmap];0.93[TSI][hapmap]
rs11070863	0.97[ASN][1000 genomes]
rs11631725	0.94[CHB][hapmap];0.87[JPT][hapmap];0.93[ASN][1000 genomes]
rs11633713	0.84[CHB][hapmap]
rs11634955	0.99[ASN][1000 genomes]
rs11635216	0.87[MEX][hapmap];0.95[TSI][hapmap]
rs11638106	0.94[CHB][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs11638154	0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs12372948	0.87[MEX][hapmap];0.95[TSI][hapmap]
rs1456299	0.94[CHB][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs1456300	0.92[ASN][1000 genomes]
rs2054166	0.94[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2124592	0.80[CEU][hapmap];0.84[CHB][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2124875	0.80[CEU][hapmap]
rs2124878	0.80[CEU][hapmap];0.83[CHB][hapmap]
rs2168474	0.83[ASN][1000 genomes]
rs2278989	0.80[CEU][hapmap];0.84[CHB][hapmap];0.93[TSI][hapmap]
rs2278990	0.84[CHB][hapmap];0.95[TSI][hapmap]
rs2305708	0.84[CHB][hapmap]
rs2305716	0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs2414105	0.87[MEX][hapmap];0.95[TSI][hapmap]
rs2414106	0.95[TSI][hapmap]
rs2414109	0.95[TSI][hapmap]
rs2607119	0.94[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs2622775	0.89[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs2652594	0.81[JPT][hapmap]
rs28576876	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2899477	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4774591	0.81[CEU][hapmap]
rs4774597	0.83[AMR][1000 genomes]
rs4774598	0.80[AMR][1000 genomes]
rs4775943	0.84[CEU][hapmap]
rs4775953	0.95[TSI][hapmap]
rs4775955	0.95[TSI][hapmap]
rs4775960	0.95[TSI][hapmap]
rs4775961	0.95[TSI][hapmap]
rs4775968	0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs55982453	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60060794	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7167760	0.80[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7168749	0.96[ASN][1000 genomes]
rs7171884	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7177471	0.84[CHB][hapmap];0.81[AMR][1000 genomes]
rs7177720	0.80[CEU][hapmap];0.95[TSI][hapmap]
rs7183479	1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs744039	0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs750162	0.84[CHB][hapmap]
rs8023455	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8030121	0.81[AMR][1000 genomes]
rs8031875	0.80[AMR][1000 genomes]
rs8033234	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8034197	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8037167	0.80[CEU][hapmap];0.84[CHB][hapmap];0.95[TSI][hapmap]
rs8037340	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs8040080	0.83[CHB][hapmap]
rs8042221	0.93[TSI][hapmap]
rs8042840	0.84[CHB][hapmap];0.95[TSI][hapmap]
rs9744054	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9944241	0.81[CEU][hapmap];0.95[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv904219	chr15:51851999-51977159	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	n/a
3	nsv457139	chr15:51854718-51977159	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	n/a
4	nsv569407	chr15:51854718-51977159	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	n/a
5	nsv1035967	chr15:51949866-52008736	Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7170980	SCG3	cis	cerebellum	SCAN
rs7170980	ARPP19	cis	parietal	SCAN
rs7170980	ATP8B4	cis	parietal	SCAN
rs7170980	DMXL2	cis	multi-tissue	Pritchard
rs7170980	DMXL2	cis	lymphoblastoid	seeQTL
rs7170980	BCL2L10	cis	parietal	SCAN
rs7170980	TMOD2	cis	parietal	SCAN
rs7170980	DMXL2	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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