Variant report

Variant	rs933856
Chromosome Location	chr15:50483736-50483737
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:50479780..50482018-chr15:50483690..50485880,3	K562	blood:
2	chr15:50481284..50485703-chr15:50645023..50648855,4	MCF-7	breast:
3	chr15:50483477..50486888-chr15:50488882..50492194,4	K562	blood:

Variant related genes	Relation type
ENSG00000244879	Chromatin interaction
ENSG00000104064	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12164938	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1365505	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1549520	0.93[YRI][hapmap]
rs1648348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1648350	0.96[ASN][1000 genomes]
rs1797313	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1797317	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1896171	0.81[AMR][1000 genomes]
rs2052759	0.88[GIH][hapmap];0.82[JPT][hapmap];0.89[LWK][hapmap]
rs2263561	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2554887	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28448616	0.83[AFR][1000 genomes]
rs4238381	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4775861	0.85[YRI][hapmap]
rs4775869	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7176501	0.84[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.82[MEX][hapmap];0.96[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7179025	0.87[LWK][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs9788756	0.82[AFR][1000 genomes];0.94[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs933856	SLC27A2	cis	cerebellum	SCAN
rs933856	SNORD116-27	trans	cerebellum	SCAN
rs933856	ATP8B4	cis	cerebellum	SCAN
rs933856	DUOX2	cis	parietal	SCAN
rs933856	FRMD5	cis	parietal	SCAN
rs933856	FGF7	cis	brain	seeQTL

Chromatin state (count:23 , 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	chr15:50477600-50486200	Enhancers	HepG2	liver
4	chr15:50477600-50498000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr15:50477600-50502200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr15:50478000-50486400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr15:50478400-50502400	Weak transcription	Placenta	Placenta
8	chr15:50478800-50487000	Enhancers	Fetal Intestine Large	intestine
9	chr15:50480000-50490000	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr15:50480400-50501600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr15:50481800-50483800	Enhancers	Primary B cells from peripheral blood	blood
12	chr15:50482000-50502800	Weak transcription	Duodenum Mucosa	Duodenum
13	chr15:50482200-50487000	Strong transcription	Hela-S3	cervix
14	chr15:50482600-50501800	Weak transcription	A549	lung
15	chr15:50482800-50492600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr15:50483000-50483800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr15:50483000-50487000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr15:50483200-50483800	Genic enhancers	Liver	Liver
19	chr15:50483200-50483800	Enhancers	Fetal Kidney	kidney
20	chr15:50483200-50485800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr15:50483200-50497400	Weak transcription	K562	blood
22	chr15:50483400-50483800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr15:50483400-50483800	Genic enhancers	Fetal Intestine Small	intestine

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