Variant report

Variant	rs9920490
Chromosome Location	chr15:50515631-50515632
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	chr15:50473021..50475909-chr15:50514369..50517198,2	MCF-7	breast:
3	chr15:50514723..50516231-chr15:50645292..50647059,2	MCF-7	breast:
4	chr15:50514272..50515874-chr15:50516020..50517695,2	MCF-7	breast:
5	chr15:50513432..50516110-chr15:50646563..50649335,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140284	Chromatin interaction
ENSG00000244879	Chromatin interaction
ENSG00000104043	Chromatin interaction
ENSG00000104064	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10519263	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13329426	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13329489	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs13329494	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1529341	1.00[JPT][hapmap]
rs1529343	1.00[JPT][hapmap]
rs1529344	0.82[JPT][hapmap]
rs1549521	0.81[ASW][hapmap];0.98[LWK][hapmap];0.88[MKK][hapmap];0.81[AFR][1000 genomes]
rs16963400	1.00[JPT][hapmap]
rs16963414	0.82[JPT][hapmap]
rs16963416	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16963420	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16963426	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16963436	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963441	0.85[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap]
rs16963451	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16963459	1.00[JPT][hapmap]
rs16963464	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17848313	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1802536	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap]
rs2414040	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28420348	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28430324	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28448432	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28465011	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28505254	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28569877	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28631084	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28715470	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28715698	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28728273	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56185295	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6493419	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6493420	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6493421	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6493422	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7162254	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7162842	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7163191	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7175274	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8024292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8029462	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs8030902	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs8035897	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8036826	0.83[EUR][1000 genomes]
rs8039502	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8040691	0.88[EUR][1000 genomes]
rs8040819	0.88[EUR][1000 genomes]
rs8041232	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8041589	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8041910	0.88[EUR][1000 genomes]
rs8043431	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9920490	ATP8B4	cis	cerebellum	SCAN
rs9920490	SLC24A5	cis	cerebellum	SCAN

Chromatin state (count:24 , 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	chr15:50513600-50516200	Weak transcription	Fetal Intestine Small	intestine
8	chr15:50513800-50525200	Weak transcription	Stomach Mucosa	stomach
9	chr15:50513800-50525400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr15:50514000-50518200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr15:50514000-50524600	Weak transcription	Primary B cells from cord blood	blood
12	chr15:50514000-50531600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr15:50514200-50516200	Enhancers	HSMM	muscle
14	chr15:50514400-50517000	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr15:50514400-50519400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr15:50514400-50530200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr15:50514600-50516000	Strong transcription	Liver	Liver
18	chr15:50514600-50519800	Weak transcription	Esophagus	oesophagus
19	chr15:50515000-50516400	Strong transcription	HepG2	liver
20	chr15:50515000-50517200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr15:50515200-50516000	Genic enhancers	K562	blood
22	chr15:50515400-50516200	Strong transcription	Fetal Intestine Large	intestine
23	chr15:50515400-50516600	Weak transcription	HSMMtube	muscle
24	chr15:50515600-50516200	Strong transcription	A549	lung

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