Variant report

Variant	rs12659261
Chromosome Location	chr5:14249610-14249611
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:14247745..14252723-chr5:14254933..14257114,4	MCF-7	breast:
2	chr5:14234443..14236446-chr5:14248979..14250681,2	MCF-7	breast:
3	chr5:14242667..14245241-chr5:14248940..14251910,2	K562	blood:
4	chr5:14245041..14247685-chr5:14248600..14251255,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11133784	0.82[JPT][hapmap]
rs11743665	1.00[ASW][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap]
rs151899	0.82[JPT][hapmap]
rs154150	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs154153	0.81[EUR][1000 genomes]
rs154154	0.81[EUR][1000 genomes]
rs154155	0.81[EUR][1000 genomes]
rs164629	0.86[JPT][hapmap]
rs164862	1.00[JPT][hapmap]
rs164863	0.95[JPT][hapmap]
rs165083	0.81[EUR][1000 genomes]
rs165094	0.81[JPT][hapmap]
rs165095	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs16903264	0.80[JPT][hapmap]
rs16903326	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16903338	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs247142	0.80[CEU][hapmap];0.83[MEX][hapmap];1.00[YRI][hapmap]
rs30603	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs30604	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs30605	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs30618	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs30621	0.81[CHB][hapmap]
rs30628	0.85[JPT][hapmap]
rs30629	0.91[JPT][hapmap]
rs30631	0.90[JPT][hapmap]
rs30783	1.00[YRI][hapmap]
rs32549	0.86[JPT][hapmap]
rs354303	0.82[JPT][hapmap]
rs39857	0.80[CEU][hapmap];1.00[YRI][hapmap]
rs42204	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs42405	0.81[EUR][1000 genomes]
rs42551	0.80[CEU][hapmap];0.91[MEX][hapmap]
rs556928	0.81[JPT][hapmap]
rs56226439	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58221971	0.83[ASN][1000 genomes]
rs6554849	0.83[ASN][1000 genomes]
rs67084079	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72744279	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7380307	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7700787	0.90[CEU][hapmap];0.95[CHB][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][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	esv1825924	chr5:14147376-14270450	Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv830209	chr5:14154989-14301758	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv948355	chr5:14160447-14395478	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1026914	chr5:14237782-14751588	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12659261	LOC285696	cis	parietal	SCAN
rs12659261	FAM105B	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14234600-14250200	Weak transcription	Placenta	Placenta
2	chr5:14238000-14250000	Weak transcription	HepG2	liver
3	chr5:14238000-14252400	Weak transcription	NHEK	skin
4	chr5:14238600-14250200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:14242600-14250200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr5:14243600-14250000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr5:14245800-14252400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr5:14246000-14249800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr5:14246000-14250000	Enhancers	Muscle Satellite Cultured Cells	--
10	chr5:14246800-14250000	Weak transcription	Thymus	Thymus
11	chr5:14247200-14249800	Weak transcription	Adipose Nuclei	Adipose
12	chr5:14247200-14250000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr5:14247200-14256800	Weak transcription	Stomach Mucosa	stomach
14	chr5:14247400-14249800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr5:14247400-14250000	Weak transcription	Liver	Liver
16	chr5:14247400-14250000	Weak transcription	HMEC	breast
17	chr5:14247400-14250200	Weak transcription	Pancreas	Pancrea
18	chr5:14247400-14254600	Weak transcription	Hela-S3	cervix
19	chr5:14247400-14257000	Weak transcription	Gastric	stomach
20	chr5:14248400-14250400	Enhancers	Osteobl	bone
21	chr5:14248400-14252000	Genic enhancers	HSMM	muscle
22	chr5:14248400-14252600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr5:14248400-14253800	Enhancers	Fetal Muscle Trunk	muscle
24	chr5:14248400-14255400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr5:14248600-14249800	Enhancers	Brain Germinal Matrix	brain
26	chr5:14248600-14249800	Enhancers	Brain Hippocampus Middle	brain
27	chr5:14248600-14250000	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr5:14248600-14250000	Enhancers	Fetal Muscle Leg	muscle
29	chr5:14248600-14250000	Enhancers	GM12878-XiMat	blood
30	chr5:14248600-14250400	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr5:14248600-14250400	Enhancers	Ovary	ovary
32	chr5:14248600-14250400	Enhancers	NH-A	brain
33	chr5:14248600-14250600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr5:14248600-14250800	Enhancers	Right Ventricle	heart
35	chr5:14248600-14251000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr5:14248600-14251000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr5:14248600-14251000	Enhancers	Left Ventricle	heart
38	chr5:14248600-14251000	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr5:14248600-14251200	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr5:14248600-14251800	Enhancers	HSMMtube	muscle
41	chr5:14248600-14255000	Enhancers	Psoas Muscle	Psoas
42	chr5:14248800-14249800	Genic enhancers	Primary B cells from cord blood	blood
43	chr5:14248800-14250600	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr5:14248800-14250600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr5:14248800-14250600	Enhancers	A549	lung
46	chr5:14248800-14251000	Enhancers	Right Atrium	heart
47	chr5:14248800-14251800	Enhancers	Spleen	Spleen
48	chr5:14248800-14253000	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr5:14248800-14253000	Enhancers	Primary B cells from peripheral blood	blood
50	chr5:14248800-14253800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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