Variant report

Variant	rs2899458
Chromosome Location	chr15:50490868-50490869
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:50483026..50488369-chr15:50490261..50492593,5	K562	blood:
2	chr15:50489598..50491308-chr15:50645723..50647745,2	MCF-7	breast:
3	chr15:50489080..50491819-chr15:50568485..50571202,2	K562	blood:
4	chr15:50483477..50486888-chr15:50488882..50492194,4	K562	blood:
5	chr15:50489847..50492729-chr15:50498593..50501909,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000244879	Chromatin interaction
ENSG00000104064	Chromatin interaction
ENSG00000140284	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10744955	1.00[JPT][hapmap]
rs11070759	1.00[JPT][hapmap]
rs11632411	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11858285	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1648345	0.93[ASN][1000 genomes]
rs1648349	0.81[ASN][1000 genomes]
rs16963406	1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs1797314	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1797315	0.84[ASN][1000 genomes]
rs1797316	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1797318	0.96[ASN][1000 genomes]
rs1797319	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1797320	0.96[ASN][1000 genomes]
rs2052759	0.84[EUR][1000 genomes]
rs2433281	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2433283	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2554884	0.96[ASN][1000 genomes]
rs2554885	0.96[ASN][1000 genomes]
rs2554886	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2555485	0.81[ASN][1000 genomes]
rs2555487	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2555488	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2555489	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs28455006	0.96[ASN][1000 genomes]
rs3825802	0.82[JPT][hapmap]
rs6493415	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8024818	0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs8029891	1.00[JPT][hapmap]
rs8031851	0.96[ASN][1000 genomes]
rs8036133	1.00[JPT][hapmap]
rs8038363	1.00[JPT][hapmap]
rs933855	0.96[ASN][1000 genomes]
rs933857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	chr15:50480400-50501600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr15:50482000-50502800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr15:50482600-50501800	Weak transcription	A549	lung
9	chr15:50482800-50492600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr15:50483200-50497400	Weak transcription	K562	blood
11	chr15:50485600-50491000	Weak transcription	Fetal Intestine Small	intestine
12	chr15:50486800-50498000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr15:50487000-50494600	Weak transcription	Fetal Intestine Large	intestine
14	chr15:50488800-50499000	Weak transcription	Small Intestine	intestine
15	chr15:50489400-50502200	Strong transcription	Hela-S3	cervix
16	chr15:50489600-50493200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr15:50489600-50497400	Strong transcription	Liver	Liver
18	chr15:50489800-50491200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr15:50490000-50500800	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr15:50490000-50501800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr15:50490400-50492200	Strong transcription	HepG2	liver

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