Variant report

Variant	rs17604615
Chromosome Location	chr5:126710956-126710957
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:126710750..126712731-chr5:126728586..126730727,2	MCF-7	breast:

Extended variants
information (count: 98 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10519929	0.85[CHD][hapmap]
rs10519930	0.85[CHD][hapmap]
rs10519936	0.85[CEU][hapmap];0.82[TSI][hapmap]
rs10519937	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs10519938	0.85[CEU][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs11743934	0.85[CEU][hapmap]
rs11949373	0.83[EUR][1000 genomes]
rs11950058	0.83[EUR][1000 genomes]
rs11950427	0.85[CEU][hapmap]
rs11952552	0.85[CEU][hapmap]
rs11952947	0.83[EUR][1000 genomes]
rs11953024	0.83[EUR][1000 genomes]
rs11958435	0.83[EUR][1000 genomes]
rs11959505	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs12233927	0.85[CEU][hapmap]
rs12234066	0.85[CEU][hapmap]
rs1363385	0.83[CEU][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs1363388	0.85[CEU][hapmap];0.82[TSI][hapmap]
rs1363631	0.85[CEU][hapmap]
rs1422318	0.85[CEU][hapmap]
rs1529467	0.83[EUR][1000 genomes]
rs17164935	1.00[CEU][hapmap];0.96[GIH][hapmap];0.85[TSI][hapmap]
rs17164979	0.83[EUR][1000 genomes]
rs17164996	0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs17165035	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs17165082	0.87[CHD][hapmap]
rs17165090	0.85[CEU][hapmap]
rs17165105	0.85[CHD][hapmap]
rs173509	0.85[EUR][1000 genomes]
rs17444885	1.00[CEU][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17604665	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17604777	0.84[CEU][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17604819	0.84[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17604882	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17604889	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17604946	1.00[CEU][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17673474	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17673517	1.00[CEU][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17673685	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17763722	1.00[CHD][hapmap]
rs17839693	0.85[CEU][hapmap]
rs17839695	0.82[EUR][1000 genomes]
rs17839697	1.00[CHD][hapmap]
rs2068168	0.84[CEU][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2408871	0.85[CEU][hapmap]
rs3756721	0.85[CEU][hapmap]
rs3812053	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3812054	0.82[ASW][hapmap];0.84[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3812055	0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs3844184	0.85[CEU][hapmap]
rs3851469	0.85[CEU][hapmap]
rs3909351	0.85[CEU][hapmap]
rs41298308	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41298312	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4563674	0.83[EUR][1000 genomes]
rs6595764	0.88[EUR][1000 genomes]
rs6595765	0.81[EUR][1000 genomes]
rs6595767	0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs6595768	0.82[ASW][hapmap];0.84[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6595769	0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs67200948	0.82[EUR][1000 genomes]
rs67854568	0.83[EUR][1000 genomes]
rs68035691	0.83[EUR][1000 genomes]
rs6874392	0.83[EUR][1000 genomes]
rs6881894	0.85[CEU][hapmap];0.82[TSI][hapmap]
rs6882034	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6888010	0.88[EUR][1000 genomes]
rs6891785	0.83[EUR][1000 genomes]
rs6892742	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72788576	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72788578	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72788581	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72788599	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72790405	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72790408	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72790410	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72790411	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72790412	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72790417	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72790418	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72790419	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72790428	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72790430	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72790433	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72790438	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72790443	0.81[EUR][1000 genomes]
rs72790444	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72790451	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72790460	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72790468	0.80[EUR][1000 genomes]
rs72790470	0.80[EUR][1000 genomes]
rs72790475	0.80[EUR][1000 genomes]
rs73786108	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7731380	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1019821	chr5:126658200-126934917	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv537894	chr5:126658200-126934917	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1032587	chr5:126691103-126826978	Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17604615	SLC12A2	cis	cerebellum	SCAN
rs17604615	PRRC1	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126691000-126746000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr5:126704000-126712400	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr5:126706200-126719400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr5:126706800-126711600	Weak transcription	Fetal Brain Female	brain
5	chr5:126707800-126725400	Weak transcription	Brain Angular Gyrus	brain
6	chr5:126707800-126729000	Weak transcription	Brain Substantia Nigra	brain
7	chr5:126707800-126731600	Weak transcription	Brain Anterior Caudate	brain
8	chr5:126710000-126711400	Weak transcription	Brain Hippocampus Middle	brain
9	chr5:126710000-126713400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr5:126710000-126713600	Weak transcription	HSMMtube	muscle
11	chr5:126710000-126715200	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr5:126710000-126721800	Weak transcription	HSMM	muscle
13	chr5:126710000-126731800	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr5:126710200-126716000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr5:126710200-126741200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr5:126710400-126711800	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr5:126710400-126715200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr5:126710400-126719600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr5:126710600-126719600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr5:126710800-126719000	Weak transcription	Fetal Muscle Leg	muscle

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