Variant report

Variant	rs12659947
Chromosome Location	chr5:80531987-80531988
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	chr5:80531823..80533359-chr5:80535137..80538128,2	K562	blood:
2	chr5:80530046..80533018-chr5:80537820..80540645,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248794	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10041138	0.81[JPT][hapmap]
rs1039326	0.82[CHB][hapmap];0.81[EUR][1000 genomes]
rs12516414	0.91[JPT][hapmap]
rs12652649	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs12653169	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12653916	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12654520	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12657721	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16876403	0.90[JPT][hapmap]
rs16878586	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2270824	0.80[JPT][hapmap]
rs2277037	0.90[JPT][hapmap]
rs2291942	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs3776980	0.81[AMR][1000 genomes]
rs4703828	0.91[JPT][hapmap]
rs4703829	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4704716	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4704717	0.90[JPT][hapmap]
rs56270508	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57802618	0.90[ASN][1000 genomes]
rs58471723	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59621118	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61696419	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv598750	chr5:80503528-80599578	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80527000-80546200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr5:80528000-80564400	Weak transcription	Hela-S3	cervix
3	chr5:80528600-80532000	Enhancers	Lung	lung
4	chr5:80529400-80532400	Weak transcription	Placenta	Placenta
5	chr5:80529400-80532400	Active TSS	Right Ventricle	heart
6	chr5:80529400-80535200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr5:80529400-80540800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr5:80529400-80541000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr5:80529400-80543400	Weak transcription	NHLF	lung
10	chr5:80529400-80544200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr5:80529400-80549400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr5:80529600-80532000	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr5:80529600-80532200	Enhancers	Adipose Nuclei	Adipose
14	chr5:80529600-80532400	Enhancers	Brain Anterior Caudate	brain
15	chr5:80529600-80535000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr5:80529600-80541000	Weak transcription	Fetal Intestine Large	intestine
17	chr5:80529600-80542800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr5:80529600-80545800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr5:80529800-80532200	Enhancers	Ovary	ovary
20	chr5:80529800-80532400	Enhancers	Brain Angular Gyrus	brain
21	chr5:80529800-80533000	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
22	chr5:80530000-80532000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr5:80530000-80532400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr5:80530000-80532600	Flanking Active TSS	Fetal Heart	heart
25	chr5:80530000-80537200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr5:80530000-80546400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr5:80530200-80532200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr5:80530200-80532200	Enhancers	Dnd41	blood
29	chr5:80530200-80532400	Enhancers	Brain Hippocampus Middle	brain
30	chr5:80530200-80541600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr5:80530200-80544000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr5:80530400-80532000	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr5:80530400-80532200	Genic enhancers	Fetal Muscle Leg	muscle
34	chr5:80530400-80532200	Flanking Active TSS	Right Atrium	heart
35	chr5:80530400-80532400	Enhancers	Brain Cingulate Gyrus	brain
36	chr5:80530400-80532400	Enhancers	Brain Substantia Nigra	brain
37	chr5:80530400-80532600	Strong transcription	Fetal Stomach	stomach
38	chr5:80530600-80532000	Enhancers	Fetal Muscle Trunk	muscle
39	chr5:80530600-80537400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr5:80530600-80542800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr5:80530600-80543000	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr5:80530600-80543800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr5:80530600-80544000	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr5:80530800-80532200	Enhancers	Colon Smooth Muscle	Colon
45	chr5:80530800-80532200	Strong transcription	Fetal Intestine Small	intestine
46	chr5:80530800-80556400	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr5:80531000-80532000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr5:80531000-80532000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr5:80531000-80532200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr5:80531000-80540200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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