Variant report

Variant	rs2909054
Chromosome Location	chr12:12623253-12623254
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	chr12:12550464..12553838-chr12:12621141..12625480,5	MCF-7	breast:
2	chr12:12601431..12605552-chr12:12620970..12623954,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271370	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10845555	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10845558	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10845564	0.83[ASN][1000 genomes]
rs10845570	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10845571	0.86[AMR][1000 genomes]
rs11054927	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11054929	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11054930	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11054931	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11054938	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12309339	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12314295	0.86[AMR][1000 genomes]
rs2417188	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2970802	0.90[ASN][1000 genomes]
rs2970803	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4763287	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7314806	0.86[AMR][1000 genomes]
rs7978266	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs888201	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs888202	0.84[AFR][1000 genomes];0.82[AMR][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	nsv898810	chr12:12600080-12627410	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv2758295	chr12:12620654-12783124	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	esv2759880	chr12:12620654-12783124	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12596000-12629800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr12:12597400-12629000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr12:12603800-12639200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr12:12604000-12628600	Weak transcription	Fetal Lung	lung
5	chr12:12607800-12629400	Weak transcription	Fetal Kidney	kidney
6	chr12:12608400-12627200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr12:12608400-12629600	Weak transcription	Colon Smooth Muscle	Colon
8	chr12:12609000-12623400	Weak transcription	A549	lung
9	chr12:12609200-12626800	Weak transcription	Fetal Muscle Trunk	muscle
10	chr12:12609800-12628400	Weak transcription	NHLF	lung
11	chr12:12610800-12658000	Weak transcription	NHDF-Ad	bronchial
12	chr12:12611000-12627800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr12:12611000-12628600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr12:12611200-12627400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr12:12611200-12629000	Weak transcription	Hela-S3	cervix
16	chr12:12613400-12625200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr12:12613400-12627400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr12:12614600-12627400	Weak transcription	Spleen	Spleen
19	chr12:12615400-12626600	Weak transcription	GM12878-XiMat	blood
20	chr12:12616400-12627400	Weak transcription	HepG2	liver
21	chr12:12616400-12629800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr12:12616600-12624600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr12:12617000-12628800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:12617400-12623400	Strong transcription	Fetal Intestine Small	intestine
25	chr12:12618200-12623600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr12:12618400-12626800	Weak transcription	K562	blood
27	chr12:12618400-12642200	Weak transcription	Stomach Mucosa	stomach
28	chr12:12618600-12624200	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr12:12618800-12626600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr12:12618800-12626800	Weak transcription	Colonic Mucosa	Colon
31	chr12:12618800-12629800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr12:12619000-12626600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr12:12619000-12629200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr12:12619000-12634000	Weak transcription	Primary hematopoietic stem cells	blood
35	chr12:12619400-12629200	Weak transcription	Right Ventricle	heart
36	chr12:12619600-12626600	Weak transcription	Liver	Liver
37	chr12:12619800-12627200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr12:12619800-12627600	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr12:12620000-12629000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:12620200-12624200	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr12:12620200-12624200	Enhancers	Adipose Nuclei	Adipose
42	chr12:12620600-12625200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr12:12621000-12625200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr12:12621000-12625200	Weak transcription	Gastric	stomach
45	chr12:12621000-12627200	Weak transcription	Dnd41	blood
46	chr12:12621000-12628200	Weak transcription	Pancreas	Pancrea
47	chr12:12621000-12628400	Weak transcription	Aorta	Aorta
48	chr12:12621000-12629000	Weak transcription	Osteobl	bone
49	chr12:12621000-12630000	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr12:12621200-12625200	Weak transcription	Esophagus	oesophagus

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