Variant report

Variant	rs12409808
Chromosome Location	chr1:113936785-113936786
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:113935271..113938235-chr1:113994077..113995754,2	MCF-7	breast:
2	chr1:113931751..113937304-chr1:113991927..113997733,10	MCF-7	breast:
3	chr1:113934736..113938053-chr1:113941345..113946073,4	K562	blood:
4	chr1:113934960..113937525-chr1:113941030..113943620,2	K562	blood:

Variant related genes	Relation type
ENSG00000232499	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs35947596	0.84[EUR][1000 genomes];0.87[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	nsv427719	chr1:113570229-114078388	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv999873	chr1:113840351-113949453	Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
3	nsv1010110	chr1:113856612-113969417	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
4	nsv1014757	chr1:113861524-113969417	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113931200-113937200	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr1:113931600-113937600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:113931800-113937400	Active TSS	Fetal Intestine Large	intestine
4	chr1:113932200-113937200	Active TSS	Fetal Intestine Small	intestine
5	chr1:113934400-113937600	Active TSS	Duodenum Mucosa	Duodenum
6	chr1:113934400-113937800	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr1:113934800-113937400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:113934800-113945200	Weak transcription	Gastric	stomach
9	chr1:113934800-113945200	Weak transcription	Left Ventricle	heart
10	chr1:113935000-113938600	Weak transcription	Stomach Mucosa	stomach
11	chr1:113935000-113939000	Weak transcription	HSMM	muscle
12	chr1:113935000-113939200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:113935200-113936800	Enhancers	Primary T cells from cord blood	blood
14	chr1:113935200-113943200	Weak transcription	HUVEC	blood vessel
15	chr1:113935200-113945400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:113935200-113949400	Weak transcription	Fetal Muscle Leg	muscle
17	chr1:113935400-113937400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:113935400-113937400	Active TSS	A549	lung
19	chr1:113935400-113939000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:113935400-113939200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:113935400-113939600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:113935400-113939800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr1:113935600-113937200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:113935600-113937200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr1:113935600-113937600	Enhancers	Fetal Brain Male	brain
26	chr1:113935600-113938800	Weak transcription	HMEC	breast
27	chr1:113935600-113938800	Weak transcription	NHEK	skin
28	chr1:113935600-113939000	Weak transcription	Osteobl	bone
29	chr1:113935600-113939200	Weak transcription	NH-A	brain
30	chr1:113935600-113939400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:113935600-113939400	Enhancers	Hela-S3	cervix
32	chr1:113935600-113941400	Weak transcription	Fetal Lung	lung
33	chr1:113935600-113941800	Weak transcription	Ovary	ovary
34	chr1:113935600-113949400	Weak transcription	Aorta	Aorta
35	chr1:113935800-113936800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr1:113936000-113936800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:113936000-113936800	Enhancers	Brain Germinal Matrix	brain
38	chr1:113936000-113936800	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr1:113936000-113937000	Enhancers	Muscle Satellite Cultured Cells	--
40	chr1:113936000-113937600	Enhancers	Colon Smooth Muscle	Colon
41	chr1:113936000-113938600	Weak transcription	Rectal Smooth Muscle	rectum
42	chr1:113936000-113939200	Weak transcription	NHLF	lung
43	chr1:113936000-113945200	Weak transcription	Right Atrium	heart
44	chr1:113936000-113952400	Weak transcription	Fetal Stomach	stomach
45	chr1:113936200-113937600	Flanking Active TSS	HepG2	liver
46	chr1:113936200-113941400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:113936400-113936800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
48	chr1:113936400-113937400	Enhancers	NHDF-Ad	bronchial
49	chr1:113936400-113937600	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr1:113936400-113937800	Flanking Active TSS	Liver	Liver

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