Variant report

Variant	rs2554887
Chromosome Location	chr15:50488859-50488860
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:50485533..50488870-chr15:50492194..50494725,4	MCF-7	breast:
2	chr15:50475267..50477449-chr15:50487507..50490048,2	K562	blood:
3	chr15:50487139..50490001-chr15:50641333..50643043,2	K562	blood:
4	chr15:50487091..50489879-chr15:50502092..50503837,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12164938	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1365505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1549520	0.89[YRI][hapmap]
rs1648348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1648350	0.94[ASN][1000 genomes]
rs1797313	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1797317	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2052759	0.82[JPT][hapmap]
rs2263561	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs28448616	0.83[AFR][1000 genomes]
rs4238381	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4775869	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7176501	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7179025	0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs933856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9788756	0.82[AFR][1000 genomes];0.90[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:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:50476000-50503400	Weak transcription	Colonic Mucosa	Colon
2	chr15:50476600-50498000	Weak transcription	Pancreas	Pancrea
3	chr15:50477600-50498000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr15:50477600-50502200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr15:50478400-50502400	Weak transcription	Placenta	Placenta
6	chr15:50480000-50490000	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr15:50480400-50501600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:50482000-50502800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr15:50482600-50501800	Weak transcription	A549	lung
10	chr15:50482800-50492600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr15:50483200-50497400	Weak transcription	K562	blood
12	chr15:50483800-50489600	Weak transcription	Liver	Liver
13	chr15:50483800-50490000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr15:50485600-50491000	Weak transcription	Fetal Intestine Small	intestine
15	chr15:50485800-50489800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr15:50486200-50490400	Weak transcription	HepG2	liver
17	chr15:50486800-50498000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr15:50487000-50489400	Weak transcription	Hela-S3	cervix
19	chr15:50487000-50489600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr15:50487000-50494600	Weak transcription	Fetal Intestine Large	intestine
21	chr15:50488800-50499000	Weak transcription	Small Intestine	intestine

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