Variant report

Variant	rs12900408
Chromosome Location	chr15:41980564-41980565
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr15:41980520-41981168	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr15:41980563-41981116	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41851006..41852814-chr15:41978575..41981340,2	K562	blood:

Variant related genes	Relation type
MIR626	TF binding region
ENSG00000092445	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10152274	1.00[EUR][1000 genomes]
rs1197656	1.00[EUR][1000 genomes]
rs1197676	1.00[EUR][1000 genomes]
rs1197678	1.00[EUR][1000 genomes]
rs1197695	1.00[EUR][1000 genomes]
rs1197696	1.00[EUR][1000 genomes]
rs1197698	1.00[EUR][1000 genomes]
rs1201692	1.00[EUR][1000 genomes]
rs1648808	1.00[EUR][1000 genomes]
rs1648812	1.00[EUR][1000 genomes]
rs6493009	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs890497	1.00[EUR][1000 genomes]
rs890499	1.00[EUR][1000 genomes]
rs890500	1.00[EUR][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	nsv1049514	chr15:41958482-42081210	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1048655	chr15:41978391-42049360	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41954400-41982800	Weak transcription	Small Intestine	intestine
2	chr15:41954600-41983800	Weak transcription	Thymus	Thymus
3	chr15:41954600-42001000	Weak transcription	Colonic Mucosa	Colon
4	chr15:41954800-41980800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr15:41955000-41988200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr15:41959400-41988600	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr15:41959400-41989000	Weak transcription	NHDF-Ad	bronchial
8	chr15:41959600-41981000	Weak transcription	Osteobl	bone
9	chr15:41961800-41990600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr15:41962000-41983800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr15:41962000-41988400	Weak transcription	Adipose Nuclei	Adipose
12	chr15:41962000-41990800	Weak transcription	NH-A	brain
13	chr15:41962000-41991200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr15:41962000-42001400	Weak transcription	Gastric	stomach
15	chr15:41962200-41984400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr15:41962200-42001000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr15:41962600-41981400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr15:41962600-41981800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr15:41962600-41983400	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr15:41962600-41983600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr15:41962600-41984000	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr15:41962600-41988400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr15:41963400-41988400	Weak transcription	Placenta	Placenta
24	chr15:41963600-41987800	Weak transcription	Primary B cells from cord blood	blood
25	chr15:41964600-41981000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr15:41964600-41982200	Weak transcription	Ovary	ovary
27	chr15:41964800-41983800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr15:41965000-41980600	Weak transcription	K562	blood
29	chr15:41965000-41982400	Weak transcription	Brain Anterior Caudate	brain
30	chr15:41966600-41984400	Weak transcription	Left Ventricle	heart
31	chr15:41966600-41988400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr15:41967600-41982600	Weak transcription	GM12878-XiMat	blood
33	chr15:41967800-41980600	Weak transcription	Dnd41	blood
34	chr15:41968400-41982200	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr15:41968800-41988600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr15:41971200-41980600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr15:41971200-41980800	Weak transcription	Colon Smooth Muscle	Colon
38	chr15:41971600-41983600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr15:41971600-41988200	Weak transcription	Fetal Thymus	thymus
40	chr15:41971600-41997400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr15:41972000-41980800	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr15:41972000-41989600	Weak transcription	Fetal Intestine Small	intestine
43	chr15:41972400-42065200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr15:41972800-41999600	Weak transcription	Fetal Brain Female	brain
45	chr15:41973200-41981000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr15:41973200-41988400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr15:41975200-41982400	Weak transcription	Hela-S3	cervix
48	chr15:41975200-41982600	Weak transcription	Primary T cells from cord blood	blood
49	chr15:41975600-41980600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr15:41975600-41980600	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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