Variant report

Variant	rs13242997
Chromosome Location	chr7:47690034-47690035
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:47679338..47681929-chr7:47689941..47692555,2	MCF-7	breast:
2	chr7:47620975..47623376-chr7:47688566..47690749,2	MCF-7	breast:
3	chr7:47672920..47677913-chr7:47686931..47690412,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136205	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10951916	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11766347	0.80[CEU][hapmap];0.84[GIH][hapmap]
rs11768009	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11770543	0.80[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap]
rs12531737	1.00[CEU][hapmap];0.84[GIH][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs12535121	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12535169	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12537656	1.00[CEU][hapmap];0.87[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13243511	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2347990	0.82[CHB][hapmap]
rs4720603	0.89[ASN][1000 genomes]
rs4724606	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4724607	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4724608	0.85[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4724610	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6969715	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7790476	0.80[CEU][hapmap];0.84[GIH][hapmap]
rs921576	0.81[CHB][hapmap]
rs965924	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13242997	PKD1L1	cis	cerebellum	SCAN
rs13242997	CDC14C	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:47686200-47690600	Enhancers	A549	lung
2	chr7:47687000-47691800	Enhancers	HSMMtube	muscle
3	chr7:47687200-47693200	Weak transcription	Left Ventricle	heart
4	chr7:47687200-47693600	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr7:47687200-47695000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr7:47687400-47690600	Weak transcription	Ovary	ovary
7	chr7:47687400-47690800	Weak transcription	Lung	lung
8	chr7:47687400-47692600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr7:47687400-47693600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr7:47687600-47693200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:47687800-47690600	Weak transcription	Placenta	Placenta
12	chr7:47688000-47690600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr7:47688000-47690800	Weak transcription	Adipose Nuclei	Adipose
14	chr7:47688000-47693200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr7:47688000-47693200	Weak transcription	Right Atrium	heart
16	chr7:47688000-47693200	Weak transcription	Spleen	Spleen
17	chr7:47688200-47691000	Weak transcription	Primary B cells from peripheral blood	blood
18	chr7:47688200-47691000	Weak transcription	HepG2	liver
19	chr7:47688200-47693400	Weak transcription	Fetal Kidney	kidney
20	chr7:47688600-47690400	Weak transcription	NHLF	lung
21	chr7:47688800-47690200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr7:47688800-47691000	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr7:47688800-47692200	Weak transcription	Primary hematopoietic stem cells	blood
24	chr7:47688800-47693400	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr7:47688800-47694000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr7:47689000-47690400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr7:47689000-47693200	Weak transcription	Fetal Muscle Leg	muscle
28	chr7:47689000-47694000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr7:47689200-47690200	Weak transcription	Fetal Muscle Trunk	muscle
30	chr7:47689200-47690600	Weak transcription	Osteobl	bone
31	chr7:47689200-47690800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr7:47689400-47690600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr7:47689600-47691000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr7:47689600-47692000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr7:47689800-47691000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr7:47689800-47694800	Enhancers	NH-A	brain
37	chr7:47690000-47695000	Enhancers	NHDF-Ad	bronchial

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