Variant report

Variant	rs10951916
Chromosome Location	chr7:47694270-47694271
allele	A/C
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	EGR1	chr7:47694223-47694672	ECC-1	luminal epithelium:	n/a	chr7:47694442-47694452
2	FOSL2	chr7:47693316-47694464	A549	lung:	n/a	n/a
3	RPC155	chr7:47693546-47694439	Hela-S3	cervix:	n/a	n/a
4	RCOR1	chr7:47693272-47694660	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:47691927..47694720-chr7:47708904..47710828,2	MCF-7	breast:

Variant related genes	Relation type
C7orf65	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11766347	0.80[CEU][hapmap];0.84[GIH][hapmap]
rs11768009	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11770543	0.80[CEU][hapmap];0.80[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs12531737	1.00[CEU][hapmap];0.84[GIH][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs12535121	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12535169	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12537656	0.82[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13242997	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]
rs13243511	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35341430	0.82[ASN][1000 genomes]
rs4720603	0.80[ASN][1000 genomes]
rs4724606	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4724607	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4724608	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4724609	0.81[CHB][hapmap]
rs4724610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6967317	0.81[ASN][1000 genomes]
rs6968969	0.81[CHB][hapmap]
rs6969715	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7790476	0.80[CEU][hapmap];0.84[GIH][hapmap]
rs965924	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]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv888003	chr7:47694270-47907214	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10951916	PKD1L1	cis	cerebellum	SCAN
rs10951916	CDC14C	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:47687200-47695000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr7:47689800-47694800	Enhancers	NH-A	brain
3	chr7:47690000-47695000	Enhancers	NHDF-Ad	bronchial
4	chr7:47690400-47694800	Enhancers	NHLF	lung
5	chr7:47690600-47695600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr7:47691600-47694400	Weak transcription	Adipose Nuclei	Adipose
7	chr7:47692200-47694600	Enhancers	HSMMtube	muscle
8	chr7:47692600-47694800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr7:47693000-47694600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr7:47693000-47694800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr7:47693200-47694800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr7:47693200-47695000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr7:47693200-47695000	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr7:47693200-47695200	Enhancers	Fetal Muscle Leg	muscle
15	chr7:47693200-47695400	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr7:47693200-47695400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr7:47693200-47695400	Enhancers	Placenta	Placenta
18	chr7:47693400-47694400	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr7:47693400-47694600	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr7:47693400-47694800	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr7:47693400-47694800	Enhancers	Fetal Muscle Trunk	muscle
22	chr7:47693400-47694800	Enhancers	HMEC	breast
23	chr7:47693400-47695000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr7:47693400-47695000	Enhancers	HSMM	muscle
25	chr7:47693400-47695400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr7:47693600-47694600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr7:47693600-47695000	Enhancers	H1 Cell Line	embryonic stem cell
28	chr7:47693600-47695000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr7:47693600-47695200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr7:47693800-47694600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr7:47693800-47694600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr7:47693800-47694600	Enhancers	Hela-S3	cervix
33	chr7:47693800-47695200	Enhancers	Muscle Satellite Cultured Cells	--
34	chr7:47693800-47695400	Enhancers	A549	lung
35	chr7:47693800-47697800	Weak transcription	HepG2	liver
36	chr7:47694000-47694800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr7:47694200-47694400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
38	chr7:47694200-47694400	Flanking Active TSS	Osteobl	bone
39	chr7:47694200-47694600	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr7:47694200-47694600	Weak transcription	Spleen	Spleen
41	chr7:47694200-47694800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr7:47694200-47694800	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr7:47694200-47694800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr7:47694200-47694800	Enhancers	Brain Germinal Matrix	brain
45	chr7:47694200-47694800	Weak transcription	Lung	lung

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