Variant report

Variant	rs12609975
Chromosome Location	chr19:39400504-39400505
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39398838..39403067-chr19:39419638..39422578,4	MCF-7	breast:
2	chr19:39339924..39344199-chr19:39398243..39400684,3	MCF-7	breast:
3	chr19:39398169..39400794-chr19:39403289..39404909,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104835	Chromatin interaction
ENSG00000128626	Chromatin interaction
ENSG00000104824	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10775533	0.90[EUR][1000 genomes]
rs11083488	0.92[EUR][1000 genomes]
rs11083489	0.85[EUR][1000 genomes]
rs11668245	0.85[EUR][1000 genomes]
rs12462710	0.81[EUR][1000 genomes]
rs4803034	0.85[EUR][1000 genomes]
rs7508411	0.85[EUR][1000 genomes]
rs9749516	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv911677	chr19:39395654-39404457	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12609975	CTC-360G5.9	cis	Nerve Tibial	GTEx

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39391200-39420800	Weak transcription	Small Intestine	intestine
2	chr19:39391400-39402200	Weak transcription	Fetal Brain Male	brain
3	chr19:39391600-39414800	Weak transcription	HMEC	breast
4	chr19:39391600-39420600	Weak transcription	Right Atrium	heart
5	chr19:39391800-39401800	Weak transcription	Fetal Lung	lung
6	chr19:39391800-39412200	Weak transcription	Osteobl	bone
7	chr19:39392400-39414800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:39392600-39406000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr19:39392600-39414600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr19:39392600-39418800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr19:39394000-39401200	Strong transcription	Fetal Intestine Small	intestine
12	chr19:39394200-39401200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr19:39394600-39401200	Strong transcription	Fetal Stomach	stomach
14	chr19:39394800-39401000	Strong transcription	Gastric	stomach
15	chr19:39394800-39401800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr19:39395000-39401000	Strong transcription	Adipose Nuclei	Adipose
17	chr19:39395000-39401200	Strong transcription	Skeletal Muscle Female	skeletal muscle
18	chr19:39395000-39401400	Strong transcription	Skeletal Muscle Male	skeletal muscle
19	chr19:39395000-39401600	Strong transcription	Fetal Muscle Leg	muscle
20	chr19:39395200-39400800	Strong transcription	Thymus	Thymus
21	chr19:39395200-39401000	Strong transcription	Brain Hippocampus Middle	brain
22	chr19:39395200-39401200	Strong transcription	Right Ventricle	heart
23	chr19:39395600-39414800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr19:39395600-39415000	Weak transcription	Hela-S3	cervix
25	chr19:39396600-39402400	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr19:39396600-39408400	Weak transcription	HepG2	liver
27	chr19:39396800-39401800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr19:39396800-39401800	Weak transcription	Stomach Mucosa	stomach
29	chr19:39396800-39412000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr19:39397000-39412200	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr19:39397400-39400800	Strong transcription	Fetal Brain Female	brain
32	chr19:39398000-39412400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr19:39398000-39420600	Weak transcription	Psoas Muscle	Psoas
34	chr19:39398200-39400600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr19:39398200-39412200	Weak transcription	Brain Angular Gyrus	brain
36	chr19:39398400-39411600	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr19:39398600-39401800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr19:39398600-39410200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr19:39398600-39415000	Weak transcription	Brain Substantia Nigra	brain
40	chr19:39398800-39401200	Weak transcription	Placenta	Placenta
41	chr19:39398800-39401800	Weak transcription	Colon Smooth Muscle	Colon
42	chr19:39398800-39401800	Weak transcription	NHLF	lung
43	chr19:39398800-39402200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr19:39398800-39402400	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr19:39398800-39402800	Weak transcription	Brain Anterior Caudate	brain
46	chr19:39398800-39403400	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr19:39398800-39403800	Weak transcription	HSMM	muscle
48	chr19:39398800-39409000	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr19:39398800-39410000	Weak transcription	HSMMtube	muscle
50	chr19:39398800-39411600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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