Variant report

Variant	rs17518014
Chromosome Location	chr12:40427674-40427675
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	chr12:40427544..40429854-chr12:40484526..40486904,2	MCF-7	breast:

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs17442095	1.00[JPT][hapmap]
rs17442346	1.00[JPT][hapmap]
rs17442353	1.00[JPT][hapmap]
rs17442490	1.00[JPT][hapmap]
rs17442882	1.00[JPT][hapmap]
rs17458257	1.00[JPT][hapmap]
rs17458745	1.00[JPT][hapmap]
rs17458773	1.00[JPT][hapmap]
rs17458974	1.00[JPT][hapmap]
rs17460894	1.00[JPT][hapmap]
rs17460992	1.00[JPT][hapmap]
rs17465716	1.00[JPT][hapmap]
rs17483502	1.00[JPT][hapmap]
rs17489225	1.00[AMR][1000 genomes]
rs17489302	1.00[AMR][1000 genomes]
rs17489379	1.00[AMR][1000 genomes]
rs17489459	1.00[JPT][hapmap]
rs17489480	1.00[JPT][hapmap]
rs17489666	1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs17489715	1.00[AMR][1000 genomes]
rs17489722	1.00[AMR][1000 genomes]
rs17489889	1.00[AMR][1000 genomes]
rs17490013	1.00[JPT][hapmap]
rs17490418	1.00[AMR][1000 genomes]
rs17490578	1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs17490585	1.00[AMR][1000 genomes]
rs17490599	1.00[AMR][1000 genomes]
rs17490620	1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs17518050	1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs17518071	1.00[AMR][1000 genomes]
rs17518183	1.00[JPT][hapmap]
rs17518204	1.00[AMR][1000 genomes]
rs17518253	1.00[AMR][1000 genomes]
rs17518273	1.00[AMR][1000 genomes]
rs17518364	1.00[AMR][1000 genomes]
rs17518427	1.00[JPT][hapmap]
rs17518441	1.00[JPT][hapmap]
rs17518476	1.00[JPT][hapmap]
rs17518672	1.00[JPT][hapmap]
rs17518735	1.00[JPT][hapmap]
rs17518770	1.00[AMR][1000 genomes]
rs17518805	1.00[AMR][1000 genomes]
rs17518992	1.00[AMR][1000 genomes]
rs17519566	1.00[AMR][1000 genomes]
rs2708450	1.00[AMR][1000 genomes]
rs2708451	1.00[AMR][1000 genomes]
rs28365202	1.00[JPT][hapmap]
rs28370603	1.00[JPT][hapmap]
rs28370641	1.00[JPT][hapmap]
rs28370650	1.00[JPT][hapmap]
rs28370657	1.00[JPT][hapmap]
rs28370688	1.00[AMR][1000 genomes]
rs28370698	1.00[JPT][hapmap]
rs28370706	1.00[JPT][hapmap]
rs28370720	1.00[JPT][hapmap]
rs28370728	1.00[JPT][hapmap]
rs28370730	1.00[JPT][hapmap]
rs28370743	1.00[JPT][hapmap]
rs28370745	1.00[AMR][1000 genomes]
rs28370748	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs28370755	1.00[AMR][1000 genomes]
rs28370758	1.00[AMR][1000 genomes]
rs28370759	1.00[JPT][hapmap]
rs28370766	1.00[JPT][hapmap]
rs28370768	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs28370770	1.00[JPT][hapmap]
rs28370776	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs28370777	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs28370778	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs28370780	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs28370782	1.00[JPT][hapmap]
rs28370783	1.00[AMR][1000 genomes]
rs28370784	1.00[JPT][hapmap]
rs28370786	1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs28370792	1.00[JPT][hapmap]
rs28370801	1.00[JPT][hapmap]
rs28370811	1.00[JPT][hapmap]
rs28370825	1.00[JPT][hapmap]
rs7306747	1.00[AMR][1000 genomes]
rs7307258	1.00[YRI][hapmap];1.00[AMR][1000 genomes]

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	nsv1046428	chr12:40226283-40439843	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv541481	chr12:40226283-40439843	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv899027	chr12:40388510-40428561	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv558597	chr12:40414631-40442892	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40394400-40448400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr12:40405400-40445200	Weak transcription	K562	blood
3	chr12:40411400-40428200	Weak transcription	Colon Smooth Muscle	Colon
4	chr12:40411400-40428600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr12:40416600-40441800	Weak transcription	Ovary	ovary
6	chr12:40419000-40428600	Weak transcription	Aorta	Aorta
7	chr12:40419000-40447600	Weak transcription	Hela-S3	cervix
8	chr12:40421600-40428000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr12:40421600-40453400	Weak transcription	Left Ventricle	heart
10	chr12:40421800-40427800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr12:40425200-40428000	Enhancers	Fetal Intestine Small	intestine
12	chr12:40425200-40429000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:40425400-40428400	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr12:40425400-40429200	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr12:40425600-40429000	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr12:40425600-40429800	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr12:40426000-40428200	Enhancers	H1 Cell Line	embryonic stem cell
18	chr12:40426000-40428800	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr12:40426000-40429000	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr12:40426200-40429000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr12:40426400-40452800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr12:40426600-40427800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr12:40426800-40428000	Enhancers	Fetal Intestine Large	intestine
24	chr12:40426800-40428000	Weak transcription	Fetal Lung	lung
25	chr12:40426800-40429000	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr12:40427000-40427800	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr12:40427000-40428000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr12:40427000-40429200	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr12:40427200-40428200	Weak transcription	Brain Germinal Matrix	brain
30	chr12:40427200-40429000	Enhancers	Stomach Mucosa	stomach
31	chr12:40427400-40428000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:40427600-40427800	Enhancers	Duodenum Smooth Muscle	Duodenum

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