Variant report

Variant	rs11856448
Chromosome Location	chr15:40012885-40012886
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40012277..40013012-chr21:25921907..25922781,2	MCF-7	breast:
2	chr15:40004259..40006236-chr15:40010388..40013115,2	MCF-7	breast:
3	chr15:40011583..40013446-chr15:40013529..40016434,2	MCF-7	breast:
4	chr15:40011315..40014662-chr15:40074849..40076901,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150667	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1004739	0.88[CHB][hapmap];0.84[CHD][hapmap]
rs1004740	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs10459607	0.93[JPT][hapmap]
rs11631570	0.81[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs11633974	0.88[CHB][hapmap]
rs11638041	0.88[CHB][hapmap]
rs11638500	0.88[CHB][hapmap]
rs11854797	0.88[CHB][hapmap]
rs11855578	0.90[CEU][hapmap];0.92[TSI][hapmap];0.98[EUR][1000 genomes]
rs11856294	0.88[CHB][hapmap]
rs11857927	0.88[CHB][hapmap];1.00[YRI][hapmap]
rs12911842	1.00[CEU][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes]
rs1320036	0.98[EUR][1000 genomes]
rs16969445	0.88[CHB][hapmap]
rs16969460	0.82[CHB][hapmap]
rs16969637	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16969640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17714733	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs1906153	0.81[CEU][hapmap];0.96[EUR][1000 genomes]
rs1906159	0.90[CEU][hapmap];0.85[TSI][hapmap];0.96[EUR][1000 genomes]
rs1906160	0.90[CEU][hapmap];0.89[TSI][hapmap];0.98[EUR][1000 genomes]
rs2008623	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2087132	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2254829	0.81[CEU][hapmap];0.84[TSI][hapmap];0.96[EUR][1000 genomes]
rs2254942	0.96[EUR][1000 genomes]
rs2254947	0.95[EUR][1000 genomes]
rs2412409	0.82[CHB][hapmap]
rs2631692	0.96[EUR][1000 genomes]
rs2631693	0.81[CEU][hapmap];0.96[EUR][1000 genomes]
rs2631695	0.81[CEU][hapmap];0.85[TSI][hapmap];0.96[EUR][1000 genomes]
rs2631696	0.96[EUR][1000 genomes]
rs2631698	0.81[CEU][hapmap];0.96[EUR][1000 genomes]
rs2631703	0.98[EUR][1000 genomes]
rs2631715	0.87[EUR][1000 genomes]
rs2664127	0.81[CEU][hapmap];0.96[EUR][1000 genomes]
rs2664130	0.81[CEU][hapmap];0.96[EUR][1000 genomes]
rs2664131	0.81[CEU][hapmap];0.96[EUR][1000 genomes]
rs3103066	0.96[EUR][1000 genomes]
rs4476147	1.00[ASW][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap]
rs56197892	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62004766	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62004768	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62004771	0.98[EUR][1000 genomes]
rs62004772	0.96[EUR][1000 genomes]
rs67426899	0.98[EUR][1000 genomes]
rs8028503	0.90[EUR][1000 genomes]
rs951358	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11856448	FSIP1	cis	parietal	SCAN
rs11856448	THBS1	cis	parietal	SCAN
rs11856448	RTF1	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40011000-40014400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:40011000-40014800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr15:40011200-40013200	Enhancers	NHEK	skin
4	chr15:40011200-40013400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr15:40011600-40013600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr15:40011600-40013600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr15:40011600-40014000	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr15:40011800-40013800	Enhancers	Primary hematopoietic stem cells	blood
9	chr15:40011800-40014400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr15:40012000-40014400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr15:40012000-40014400	Enhancers	HMEC	breast
12	chr15:40012200-40014000	Enhancers	HSMM	muscle
13	chr15:40012600-40013400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr15:40012600-40013400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr15:40012600-40013600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr15:40012600-40014800	Enhancers	Fetal Muscle Leg	muscle
17	chr15:40012800-40013000	Flanking Active TSS	Osteobl	bone
18	chr15:40012800-40013200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr15:40012800-40013200	Active TSS	NHDF-Ad	bronchial
20	chr15:40012800-40013400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr15:40012800-40014000	Enhancers	Muscle Satellite Cultured Cells	--
22	chr15:40012800-40014000	Weak transcription	Placenta	Placenta
23	chr15:40012800-40014000	Flanking Active TSS	NH-A	brain

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