Variant report

Variant	rs2973051
Chromosome Location	chr5:37813540-37813541
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:37807892..37810201-chr5:37812921..37814976,2	MCF-7	breast:
2	chr5:37810386..37812251-chr5:37813012..37814554,2	MCF-7	breast:
3	chr5:37805427..37807575-chr5:37812355..37814098,2	MCF-7	breast:
4	chr5:37811779..37814008-chr5:37847060..37848825,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GDNF-3	chr5:37812779-37814191	NONHSAT101069

Extended variants
information (count: 9 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs2910708	0.89[ASN][1000 genomes]
rs2910712	0.98[ASN][1000 genomes]
rs2910713	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2973048	0.87[ASN][1000 genomes]
rs2973049	0.82[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.88[ASN][1000 genomes]
rs2973050	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.91[ASN][1000 genomes]
rs2973060	0.89[AMR][1000 genomes];0.86[EUR][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	nsv949716	chr5:37179341-37967352	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
2	nsv597846	chr5:37430215-37813591	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2973051	PPARA	trans	cerebellum	SCAN
rs2973051	UGT3A2	cis	cerebellum	SCAN
rs2973051	NIPBL	cis	cerebellum	SCAN
rs2973051	DHX33	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:37810600-37814200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:37810600-37815200	Weak transcription	NHLF	lung
3	chr5:37810800-37816600	Weak transcription	Brain Substantia Nigra	brain
4	chr5:37811000-37816600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr5:37811200-37817200	Weak transcription	Fetal Muscle Leg	muscle
6	chr5:37811200-37818200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr5:37811400-37814000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr5:37811400-37816400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr5:37811600-37814000	Weak transcription	HMEC	breast
10	chr5:37811800-37813800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr5:37811800-37814800	Weak transcription	NHEK	skin
12	chr5:37812000-37816200	Strong transcription	Fetal Stomach	stomach
13	chr5:37812200-37814200	Weak transcription	NH-A	brain
14	chr5:37812200-37814800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr5:37812200-37815000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr5:37812200-37816400	Weak transcription	HSMM	muscle
17	chr5:37812200-37822200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr5:37812400-37815200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr5:37812400-37815200	Weak transcription	Ovary	ovary
20	chr5:37812400-37816600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr5:37812400-37816800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:37812600-37816400	Strong transcription	Osteobl	bone
23	chr5:37812600-37816600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr5:37812800-37814200	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr5:37812800-37814800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr5:37812800-37815200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr5:37812800-37816200	Strong transcription	HSMMtube	muscle
28	chr5:37812800-37817200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr5:37813000-37816200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr5:37813000-37816400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr5:37813000-37816600	Weak transcription	Placenta	Placenta
32	chr5:37813200-37814200	Weak transcription	Colon Smooth Muscle	Colon
33	chr5:37813200-37815000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr5:37813200-37815000	Strong transcription	Fetal Intestine Small	intestine
35	chr5:37813400-37814000	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr5:37813400-37816200	Strong transcription	NHDF-Ad	bronchial
37	chr5:37813400-37824400	Weak transcription	Fetal Kidney	kidney

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