Variant report

Variant	rs413449
Chromosome Location	chr8:86459280-86459281
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	chr8:86457982..86459592-chr8:86459757..86463318,3	MCF-7	breast:

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1021457	1.00[ASN][1000 genomes]
rs1021458	1.00[ASN][1000 genomes]
rs11777530	1.00[ASW][hapmap];1.00[ASN][1000 genomes]
rs11780942	1.00[ASN][1000 genomes]
rs13265202	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13274009	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1389246	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1472200	1.00[ASN][1000 genomes]
rs1493301	1.00[ASW][hapmap];0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs17741410	1.00[ASN][1000 genomes]
rs17814183	1.00[ASN][1000 genomes]
rs17814255	1.00[ASN][1000 genomes]
rs17814594	1.00[ASN][1000 genomes]
rs1979694	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2101706	1.00[ASN][1000 genomes]
rs2201258	1.00[ASN][1000 genomes]
rs2466764	1.00[ASN][1000 genomes]
rs2645050	1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs2725292	1.00[YRI][hapmap]
rs2725295	1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs2725296	1.00[YRI][hapmap]
rs359523	1.00[ASN][1000 genomes]
rs359526	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs359527	0.95[EUR][1000 genomes]
rs359530	1.00[ASN][1000 genomes]
rs359536	1.00[ASN][1000 genomes]
rs36054079	1.00[ASN][1000 genomes]
rs370167	1.00[ASN][1000 genomes]
rs384656	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs385064	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs393828	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs395964	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs404123	1.00[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs406858	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs407320	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs411276	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs414354	1.00[ASN][1000 genomes]
rs414922	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs415199	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs422914	1.00[ASN][1000 genomes]
rs427285	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs435449	0.93[CEU][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs438730	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs443177	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs447131	1.00[ASN][1000 genomes]
rs4740052	1.00[ASN][1000 genomes]
rs56698727	1.00[ASN][1000 genomes]
rs62512497	1.00[ASN][1000 genomes]
rs62512498	1.00[ASN][1000 genomes]
rs650498	1.00[ASN][1000 genomes]
rs6605618	1.00[ASW][hapmap];1.00[ASN][1000 genomes]
rs6605621	1.00[ASN][1000 genomes]
rs663323	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6984702	1.00[ASN][1000 genomes]
rs6990339	1.00[ASN][1000 genomes]
rs6994366	1.00[ASW][hapmap];1.00[ASN][1000 genomes]
rs6999266	1.00[ASN][1000 genomes]
rs7823943	1.00[ASN][1000 genomes]
rs7844166	1.00[ASN][1000 genomes]
rs981495	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018483	chr8:86142258-86547831	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv1022463	chr8:86257031-86547831	Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	esv1804888	chr8:86263098-86986703	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1028148	chr8:86310570-86553130	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	esv2761206	chr8:86310582-86468868	Enhancers Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	esv1807380	chr8:86405478-86886412	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	esv1829254	chr8:86405478-86886412	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	esv1831796	chr8:86405478-86886412	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	esv1807498	chr8:86405478-86986703	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	esv1828364	chr8:86405478-86986703	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
11	esv1831268	chr8:86405478-86986703	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
12	esv1844000	chr8:86405478-86986703	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
13	esv1851686	chr8:86405478-86986703	ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
14	nsv427824	chr8:86405478-86986703	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
15	esv2758162	chr8:86405478-87055053	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
16	esv2759624	chr8:86405478-87055053	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
17	nsv428204	chr8:86405478-87312208	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
18	nsv891122	chr8:86415959-86513414	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
19	nsv831378	chr8:86433343-86569655	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
20	nsv891123	chr8:86434228-86572238	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
21	nsv891124	chr8:86440705-86553992	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
22	nsv891125	chr8:86453838-86778025	Weak transcription ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
23	nsv891126	chr8:86456595-86547351	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs413449	PSKH2	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:86457000-86463400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr8:86458200-86459400	Flanking Active TSS	Liver	Liver
3	chr8:86458400-86459400	Enhancers	Brain Angular Gyrus	brain
4	chr8:86458400-86459600	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr8:86458400-86459600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr8:86458400-86459800	Enhancers	Duodenum Mucosa	Duodenum
7	chr8:86458400-86459800	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr8:86458400-86459800	Enhancers	Pancreas	Pancrea
9	chr8:86458400-86459800	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr8:86458400-86459800	Enhancers	HepG2	liver
11	chr8:86458400-86460000	Enhancers	Rectal Mucosa Donor 29	rectum
12	chr8:86458400-86462400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr8:86458800-86462400	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr8:86458800-86462600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr8:86458800-86462600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr8:86459000-86459600	Flanking Active TSS	A549	lung
17	chr8:86459000-86462600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr8:86459000-86462600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr8:86459000-86468800	Weak transcription	Brain Anterior Caudate	brain
20	chr8:86459200-86459600	Flanking Active TSS	Stomach Mucosa	stomach
21	chr8:86459200-86459800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr8:86459200-86459800	Enhancers	Fetal Intestine Large	intestine
23	chr8:86459200-86462400	Weak transcription	Brain Hippocampus Middle	brain
24	chr8:86459200-86462600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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