Variant report

Variant	rs6945000
Chromosome Location	chr7:47941357-47941358
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs13246713	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2708906	0.83[JPT][hapmap]
rs28733677	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34439423	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35389440	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35588446	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6945365	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7791003	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7792708	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs939906	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv869585	chr7:47765428-48151324	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv830991	chr7:47854530-48025996	Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv532120	chr7:47882757-48195869	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv470221	chr7:47917495-48354363	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv464442	chr7:47917495-48354820	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv606893	chr7:47917495-48354820	Flanking Active TSS Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6945000	NACAD	cis	parietal	SCAN
rs6945000	UPP1	cis	cerebellum	SCAN
rs6945000	PKD1L1	cis	parietal	SCAN
rs6945000	PKD1L1	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:47903400-47945000	Weak transcription	Brain Angular Gyrus	brain
2	chr7:47916400-47949000	Weak transcription	Right Ventricle	heart
3	chr7:47925600-47946800	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr7:47927400-47945000	Weak transcription	Brain Anterior Caudate	brain
5	chr7:47928200-47945000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr7:47928400-47957600	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr7:47929600-47947000	Weak transcription	Left Ventricle	heart
8	chr7:47930400-47945600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr7:47934000-48001800	Weak transcription	Psoas Muscle	Psoas
10	chr7:47937000-47944000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr7:47937000-47944400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr7:47937800-47944600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr7:47937800-47945000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr7:47937800-47945000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr7:47938000-47944400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr7:47939200-47943800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr7:47940000-47942800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr7:47941000-47941400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr7:47941000-47941400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr7:47941000-47941400	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr7:47941000-47941800	Enhancers	HSMMtube	muscle
22	chr7:47941000-47942000	Enhancers	Muscle Satellite Cultured Cells	--
23	chr7:47941000-47942000	Enhancers	HSMM	muscle
24	chr7:47941000-47942200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr7:47941000-47942200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr7:47941000-47942200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr7:47941000-47942200	Enhancers	NHDF-Ad	bronchial
28	chr7:47941000-47942200	Enhancers	Osteobl	bone
29	chr7:47941000-47942400	Enhancers	Adipose Nuclei	Adipose
30	chr7:47941000-47942600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr7:47941000-47942600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr7:47941200-47941400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr7:47941200-47941400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr7:47941200-47941400	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr7:47941200-47941400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr7:47941200-47941400	Flanking Active TSS	Hela-S3	cervix
37	chr7:47941200-47941600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr7:47941200-47941800	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr7:47941200-47941800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr7:47941200-47942000	Enhancers	NH-A	brain
41	chr7:47941200-47942200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr7:47941200-47942200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr7:47941200-47944000	Weak transcription	Lung	lung

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