Variant report

Variant	rs12440789
Chromosome Location	chr15:50517531-50517532
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:50515572..50518632-chr15:50523853..50526982,3	K562	blood:
2	chr15:50512449..50514505-chr15:50516490..50518212,2	K562	blood:
3	chr15:50514272..50515874-chr15:50516020..50517695,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000200605	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2853766	0.84[CEU][hapmap];0.83[JPT][hapmap];0.80[EUR][1000 genomes]
rs59627287	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs854150	0.94[JPT][hapmap]
rs854151	0.82[CHB][hapmap];0.94[JPT][hapmap];0.86[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	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1035983	chr15:50223334-50595170	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv542382	chr15:50223334-50595170	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50503600-50519800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr15:50503600-50539800	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr15:50508000-50539800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr15:50511800-50525400	Strong transcription	Hela-S3	cervix
5	chr15:50512000-50519200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr15:50512800-50530000	Weak transcription	Colonic Mucosa	Colon
7	chr15:50513800-50525200	Weak transcription	Stomach Mucosa	stomach
8	chr15:50513800-50525400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr15:50514000-50518200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr15:50514000-50524600	Weak transcription	Primary B cells from cord blood	blood
11	chr15:50514000-50531600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:50514400-50519400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr15:50514400-50530200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr15:50514600-50519800	Weak transcription	Esophagus	oesophagus
15	chr15:50515800-50537200	Weak transcription	Gastric	stomach
16	chr15:50516000-50519400	Weak transcription	K562	blood
17	chr15:50516200-50519000	Weak transcription	A549	lung
18	chr15:50516200-50519000	Weak transcription	HSMM	muscle
19	chr15:50516200-50519400	Weak transcription	Fetal Intestine Large	intestine
20	chr15:50516400-50517800	Weak transcription	HepG2	liver
21	chr15:50516400-50519400	Weak transcription	Fetal Intestine Small	intestine
22	chr15:50517000-50518000	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr15:50517200-50519000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr15:50517200-50519000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr15:50517200-50519200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr15:50517200-50519200	Enhancers	Liver	Liver

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