Variant report

Variant	rs1241645
Chromosome Location	chr14:25347522-25347523
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	chr14:25347366..25347980-chr8:125299505..125300432,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1241605	0.96[CEU][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs1241608	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs1241615	0.88[CEU][hapmap];0.80[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs1241616	0.88[CEU][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs1241617	0.88[CEU][hapmap];0.80[CHB][hapmap];0.89[EUR][1000 genomes]
rs1241618	0.88[CEU][hapmap];0.80[CHB][hapmap];0.89[EUR][1000 genomes]
rs1241619	0.88[CEU][hapmap];0.80[CHB][hapmap];0.89[EUR][1000 genomes]
rs1241620	0.88[CEU][hapmap];0.80[CHB][hapmap];0.89[EUR][1000 genomes]
rs1241621	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs1241622	0.88[CEU][hapmap];0.80[CHB][hapmap];0.89[EUR][1000 genomes]
rs1241623	0.89[EUR][1000 genomes]
rs1241625	0.88[CEU][hapmap];0.80[CHB][hapmap];0.89[EUR][1000 genomes]
rs1241626	0.89[EUR][1000 genomes]
rs1241627	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs1241628	0.89[EUR][1000 genomes]
rs1241629	0.88[CEU][hapmap];0.80[CHB][hapmap];0.89[EUR][1000 genomes]
rs1241630	0.89[EUR][1000 genomes]
rs1241631	0.88[CEU][hapmap];0.80[CHB][hapmap];0.89[EUR][1000 genomes]
rs1241632	0.88[CEU][hapmap];0.80[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs1241634	0.92[CEU][hapmap];0.80[CHB][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1241644	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1312629	0.88[CEU][hapmap];0.80[CHB][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1312630	0.88[CEU][hapmap];0.80[CHB][hapmap];0.89[EUR][1000 genomes]
rs1312631	0.88[CEU][hapmap];0.80[CHB][hapmap];0.89[EUR][1000 genomes]
rs1312632	0.88[CEU][hapmap];0.80[CHB][hapmap];0.86[EUR][1000 genomes]
rs2104281	0.86[EUR][1000 genomes]
rs2332448	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs2614511	0.88[EUR][1000 genomes]
rs2771289	0.88[EUR][1000 genomes]
rs6574078	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6574079	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs712491	0.90[MEX][hapmap]
rs7143584	0.96[CEU][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs8017040	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs854391	0.85[MEX][hapmap]
rs854396	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041336	chr14:24726564-25527319	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542000	chr14:24726564-25527319	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv901504	chr14:25184210-25646203	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv901505	chr14:25237268-25360584	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv901506	chr14:25295551-25377188	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1041445	chr14:25326692-25388290	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv1810592	chr14:25346636-25354756	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1241645	SLC39A2	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:25331000-25349800	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr14:25331200-25349800	Weak transcription	HSMM	muscle
3	chr14:25342800-25351000	Enhancers	Brain Substantia Nigra	brain
4	chr14:25343000-25351200	Enhancers	Brain Cingulate Gyrus	brain
5	chr14:25343200-25349000	Weak transcription	Right Atrium	heart
6	chr14:25343200-25349600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr14:25343800-25347600	Enhancers	Brain Angular Gyrus	brain
8	chr14:25344000-25351000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr14:25344400-25348800	Weak transcription	Fetal Muscle Trunk	muscle
10	chr14:25344400-25349000	Weak transcription	Left Ventricle	heart
11	chr14:25344400-25349000	Weak transcription	Lung	lung
12	chr14:25344600-25354200	Weak transcription	Fetal Intestine Large	intestine
13	chr14:25344800-25349400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr14:25344800-25349600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr14:25345200-25348800	Weak transcription	Fetal Heart	heart
16	chr14:25345200-25349200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr14:25345400-25349400	Weak transcription	NHDF-Ad	bronchial
18	chr14:25345600-25349000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr14:25345800-25349000	Weak transcription	Pancreas	Pancrea
20	chr14:25345800-25349000	Weak transcription	Right Ventricle	heart
21	chr14:25345800-25349600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr14:25346000-25349000	Weak transcription	Fetal Muscle Leg	muscle
23	chr14:25346000-25349000	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr14:25346000-25358000	Weak transcription	Fetal Intestine Small	intestine
25	chr14:25346200-25347600	Enhancers	Brain Hippocampus Middle	brain
26	chr14:25346200-25348800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr14:25346200-25349200	Weak transcription	Colon Smooth Muscle	Colon
28	chr14:25346200-25350400	Weak transcription	Stomach Mucosa	stomach
29	chr14:25346200-25351200	Enhancers	Brain Anterior Caudate	brain
30	chr14:25346400-25348800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr14:25346400-25348800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr14:25346400-25350400	Weak transcription	Fetal Stomach	stomach
33	chr14:25346600-25347800	Weak transcription	HepG2	liver
34	chr14:25346800-25348000	Weak transcription	Adipose Nuclei	Adipose
35	chr14:25346800-25349600	Weak transcription	Fetal Lung	lung
36	chr14:25346800-25350400	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr14:25347000-25349000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr14:25347000-25349000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr14:25347200-25350200	Weak transcription	Rectal Smooth Muscle	rectum

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