Variant report

Variant	rs2587550
Chromosome Location	chr11:113272925-113272926
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr11:113272532-113272944	SK-N-SH	brain:	n/a	chr11:113272725-113272735 chr11:113272717-113272733 chr11:113272727-113272734
2	MXI1	chr11:113272286-113273148	SK-N-SH	brain:	n/a	n/a
3	NFIC	chr11:113272369-113272976	ECC-1	luminal epithelium:	n/a	n/a
4	FOS	chr11:113272419-113272944	MCF10A-Er-Src	breast:	n/a	chr11:113272598-113272607
5	MYC	chr11:113272472-113272995	MCF10A-Er-Src	breast:	n/a	chr11:113272725-113272735 chr11:113272717-113272733 chr11:113272727-113272734
6	MYC	chr11:113272485-113272942	MCF10A-Er-Src	breast:	n/a	chr11:113272725-113272735 chr11:113272717-113272733 chr11:113272727-113272734
7	MAX	chr11:113272457-113272944	MCF-7	breast:	n/a	chr11:113272725-113272735 chr11:113272717-113272733 chr11:113272727-113272734
8	MAX	chr11:113272475-113272937	MCF-7	breast:	n/a	chr11:113272725-113272735 chr11:113272717-113272733 chr11:113272727-113272734

Variant related genes	Relation type
ENSG00000256757	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1003641	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1076560	0.81[CHD][hapmap]
rs1076562	0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs1079595	0.83[CHB][hapmap]
rs10891545	0.87[CHD][hapmap];0.83[JPT][hapmap]
rs11214598	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11214601	0.83[CHB][hapmap]
rs11214602	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1124491	0.83[CHB][hapmap]
rs1124492	0.89[CHD][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs1124493	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12224538	0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs1800497	0.83[CHB][hapmap];0.91[CHD][hapmap]
rs2002453	0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs2005313	0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs2242592	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2245805	0.95[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs2471856	0.88[ASN][1000 genomes]
rs2511521	0.92[ASN][1000 genomes]
rs2587552	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2734841	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2734842	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2734849	0.84[YRI][hapmap]
rs2859543	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2859544	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2859545	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4586205	0.86[JPT][hapmap]
rs4590907	0.88[CHD][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs4938014	0.88[CHD][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs4938016	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61492892	0.83[ASN][1000 genomes]
rs6275	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6278	0.83[CHB][hapmap];0.91[CHD][hapmap]
rs6279	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7118900	0.89[CHD][hapmap]
rs7122228	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv556444	chr11:113234432-113383394	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1040152	chr11:113258065-113285916	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv515795	chr11:113266821-113272925	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2587550	TTC12	cis	lesional skin	skin_eQTL
rs2587550	TTC12	cis	parietal	SCAN
rs2587550	TTC12	cis	Heart Left Ventricle	GTEx
rs2587550	SIK3	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:113258800-113287400	Weak transcription	Gastric	stomach
2	chr11:113259200-113276000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:113270600-113275200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr11:113271600-113273000	Enhancers	Spleen	Spleen
5	chr11:113271800-113273200	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr11:113271800-113273400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr11:113271800-113273600	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr11:113272000-113273000	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr11:113272000-113273000	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr11:113272000-113273200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr11:113272000-113273200	Enhancers	Brain Germinal Matrix	brain
12	chr11:113272000-113273400	Enhancers	HMEC	breast
13	chr11:113272200-113273000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr11:113272200-113273000	Enhancers	Right Ventricle	heart
15	chr11:113272200-113273000	Enhancers	NHEK	skin
16	chr11:113272200-113273200	Enhancers	HSMMtube	muscle
17	chr11:113272200-113273400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr11:113272400-113273000	Enhancers	Muscle Satellite Cultured Cells	--
19	chr11:113272400-113273000	Enhancers	Brain Anterior Caudate	brain
20	chr11:113272400-113273000	Enhancers	Brain Cingulate Gyrus	brain
21	chr11:113272400-113273000	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr11:113272400-113273000	Enhancers	Brain Substantia Nigra	brain
23	chr11:113272400-113273000	Enhancers	Fetal Brain Male	brain
24	chr11:113272400-113273000	Enhancers	Fetal Muscle Leg	muscle
25	chr11:113272400-113273200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr11:113272400-113275800	Weak transcription	Esophagus	oesophagus
27	chr11:113272600-113273000	Enhancers	Fetal Brain Female	brain
28	chr11:113272600-113273600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr11:113272800-113273000	Enhancers	Brain Angular Gyrus	brain
30	chr11:113272800-113273000	Enhancers	HSMM	muscle

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