Variant report

Variant	rs965924
Chromosome Location	chr7:47687938-47687939
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:47685575..47687990-chr7:47705109..47707807,2	MCF-7	breast:
2	chr7:47687164..47688897-chr7:47693209..47694904,2	MCF-7	breast:
3	chr7:47687322..47690027-chr7:47714537..47716150,2	MCF-7	breast:
4	chr7:47681304..47684900-chr7:47685639..47688597,3	MCF-7	breast:
5	chr7:47672920..47677913-chr7:47686931..47690412,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000221845	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

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];0.97[GIH][hapmap];0.89[JPT][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11766347	0.80[CEU][hapmap];0.81[GIH][hapmap]
rs11768009	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11770543	0.80[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap]
rs12531737	1.00[CEU][hapmap];0.81[GIH][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs12535121	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12535169	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12537656	1.00[CEU][hapmap];0.84[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13242997	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]
rs13243511	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2347990	0.82[CHB][hapmap]
rs4720603	0.89[ASN][1000 genomes]
rs4724606	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4724607	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4724608	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4724610	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6969715	1.00[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7790476	0.80[CEU][hapmap];0.81[GIH][hapmap]
rs921576	0.81[CHB][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs965924	PKD1L1	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:47685600-47688200	Enhancers	Primary B cells from peripheral blood	blood
2	chr7:47685800-47688200	Enhancers	Fetal Intestine Large	intestine
3	chr7:47686200-47688000	Enhancers	Primary B cells from cord blood	blood
4	chr7:47686200-47688200	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr7:47686200-47688200	Enhancers	Fetal Thymus	thymus
6	chr7:47686200-47688800	Enhancers	Primary hematopoietic stem cells	blood
7	chr7:47686200-47690600	Enhancers	A549	lung
8	chr7:47686400-47688000	Enhancers	Primary T cells from cord blood	blood
9	chr7:47686400-47688000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr7:47686400-47688400	Enhancers	Fetal Muscle Leg	muscle
11	chr7:47686400-47688800	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr7:47686600-47688000	Enhancers	Fetal Stomach	stomach
13	chr7:47686600-47688000	Enhancers	Right Atrium	heart
14	chr7:47686600-47688000	Enhancers	Thymus	Thymus
15	chr7:47686600-47688200	Enhancers	Fetal Heart	heart
16	chr7:47686800-47688000	Enhancers	Adipose Nuclei	Adipose
17	chr7:47686800-47689400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr7:47687000-47688000	Enhancers	Spleen	Spleen
19	chr7:47687000-47689800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr7:47687000-47691800	Enhancers	HSMMtube	muscle
21	chr7:47687200-47688000	Weak transcription	NHLF	lung
22	chr7:47687200-47688200	Enhancers	Fetal Kidney	kidney
23	chr7:47687200-47689000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr7:47687200-47689200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr7:47687200-47689200	Enhancers	Osteobl	bone
26	chr7:47687200-47689600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr7:47687200-47689800	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr7:47687200-47693200	Weak transcription	Left Ventricle	heart
29	chr7:47687200-47693600	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr7:47687200-47695000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr7:47687400-47688200	Enhancers	HepG2	liver
32	chr7:47687400-47688800	Weak transcription	Fetal Muscle Trunk	muscle
33	chr7:47687400-47688800	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr7:47687400-47689600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr7:47687400-47690600	Weak transcription	Ovary	ovary
36	chr7:47687400-47690800	Weak transcription	Lung	lung
37	chr7:47687400-47692600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr7:47687400-47693600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr7:47687600-47688000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr7:47687600-47688200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr7:47687600-47688200	Enhancers	Fetal Lung	lung
42	chr7:47687600-47689000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr7:47687600-47693200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr7:47687800-47688000	Enhancers	Brain Hippocampus Middle	brain
45	chr7:47687800-47688000	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr7:47687800-47690600	Weak transcription	Placenta	Placenta

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