Variant report

Variant	rs11856227
Chromosome Location	chr15:41158588-41158589
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:41156188..41160579-chr15:41164081..41167959,6	K562	blood:
2	chr15:41135972..41139917-chr15:41154366..41159199,4	K562	blood:
3	chr15:41154663..41156946-chr15:41157971..41160797,2	K562	blood:
4	chr15:41148610..41153040-chr15:41153153..41159814,9	MCF-7	breast:
5	chr15:41149030..41159900-chr15:41180834..41187281,18	MCF-7	breast:
6	chr15:41156581..41159555-chr15:41176856..41179338,2	MCF-7	breast:
7	chr15:41158277..41161838-chr15:41183042..41188176,5	MCF-7	breast:
8	chr15:41148133..41159834-chr15:41169228..41175193,12	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000104140	Chromatin interaction
ENSG00000104142	Chromatin interaction
ENSG00000264256	Chromatin interaction
ENSG00000166145	Chromatin interaction
ENSG00000261183	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11070298	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11070299	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070304	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11070305	0.82[ASN][1000 genomes]
rs11855507	0.82[ASN][1000 genomes]
rs12148515	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12148523	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12903603	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12916961	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16971157	1.00[CEU][hapmap]
rs1814692	0.96[EUR][1000 genomes]
rs2279578	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2412571	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28444382	0.89[EUR][1000 genomes]
rs4244581	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4384588	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4923885	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4923886	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4923887	0.90[EUR][1000 genomes]
rs4924509	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4924510	0.87[ASN][1000 genomes]
rs601436	1.00[CEU][hapmap];0.92[GIH][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes]
rs616606	0.85[EUR][1000 genomes]
rs617377	0.89[EUR][1000 genomes]
rs618892	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs618916	0.87[EUR][1000 genomes]
rs625058	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs686038	0.82[CHB][hapmap];0.92[CHD][hapmap];0.83[JPT][hapmap]
rs690507	0.89[EUR][1000 genomes]
rs7172280	1.00[CEU][hapmap]
rs8024861	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs8024961	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs8028660	0.88[CEU][hapmap];0.92[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8042095	0.84[EUR][1000 genomes]
rs9806683	0.91[CHB][hapmap];0.92[CHD][hapmap];0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv904102	chr15:41046883-41201699	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv1054764	chr15:41068625-41196410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv569228	chr15:41106485-41194151	Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	nsv904103	chr15:41123172-41275014	Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
7	nsv904104	chr15:41149824-41234932	Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv904105	chr15:41149824-41275014	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11856227	SPINT1	cis	multi-tissue	Pritchard

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41137400-41165800	Weak transcription	Right Atrium	heart
2	chr15:41150000-41165600	Weak transcription	Spleen	Spleen
3	chr15:41151600-41165400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr15:41152000-41163800	Weak transcription	Gastric	stomach
5	chr15:41153600-41159200	Enhancers	Stomach Mucosa	stomach
6	chr15:41154000-41162400	Weak transcription	GM12878-XiMat	blood
7	chr15:41155800-41159000	Enhancers	Pancreas	Pancrea
8	chr15:41156000-41159000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr15:41156200-41164000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr15:41156600-41163600	Weak transcription	Fetal Intestine Small	intestine
11	chr15:41157600-41158800	Enhancers	NHEK	skin
12	chr15:41157600-41161800	Weak transcription	Esophagus	oesophagus
13	chr15:41158000-41158600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr15:41158000-41158600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr15:41158000-41158600	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr15:41158000-41158600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr15:41158000-41158600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr15:41158000-41158600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr15:41158200-41158600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr15:41158200-41158600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr15:41158200-41158600	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr15:41158200-41158600	Enhancers	Duodenum Mucosa	Duodenum
23	chr15:41158200-41158600	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr15:41158200-41158600	Flanking Active TSS	A549	lung
25	chr15:41158200-41158600	Bivalent Enhancer	HepG2	liver
26	chr15:41158200-41158600	Enhancers	NH-A	brain
27	chr15:41158200-41158800	Enhancers	Placenta Amnion	Placenta Amnion
28	chr15:41158200-41158800	Flanking Active TSS	Hela-S3	cervix
29	chr15:41158200-41159000	Enhancers	HMEC	breast
30	chr15:41158400-41158600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr15:41158400-41158600	Bivalent Enhancer	Colonic Mucosa	Colon
32	chr15:41158400-41158600	Enhancers	Fetal Thymus	thymus
33	chr15:41158400-41158600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

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