Variant report

Variant	rs11111
Chromosome Location	chr5:37814102-37814103
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:37807892..37810201-chr5:37812921..37814976,2	MCF-7	breast:
2	chr5:37810386..37812251-chr5:37813012..37814554,2	MCF-7	breast:

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

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10069455	0.95[ASN][1000 genomes]
rs10071586	1.00[ASN][1000 genomes]
rs10076344	0.93[ASN][1000 genomes]
rs10076391	0.95[ASN][1000 genomes]
rs10473069	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12055296	0.98[ASN][1000 genomes]
rs13361833	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2910697	1.00[CHB][hapmap]
rs2910701	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2910705	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2910706	0.91[ASN][1000 genomes]
rs2910707	0.92[ASN][1000 genomes]
rs2910797	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2973045	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs2973046	0.91[ASN][1000 genomes]
rs2973047	0.92[ASN][1000 genomes]
rs2975100	1.00[CHB][hapmap];0.82[CHD][hapmap]
rs60025605	0.96[ASN][1000 genomes]
rs67720228	0.91[ASN][1000 genomes]
rs884344	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9292674	1.00[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.96[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	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	nsv516769	chr5:37814102-37814148	Enhancers Strong transcription Weak transcription Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11111	SLC1A3	cis	parietal	SCAN
rs11111	DMAP1	cis	Frontal Cortex	GTEx
rs11111	GDNF	cis	cerebellum	SCAN

Chromatin state (count:39 , 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	chr5:37811400-37816400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr5:37811800-37814800	Weak transcription	NHEK	skin
9	chr5:37812000-37816200	Strong transcription	Fetal Stomach	stomach
10	chr5:37812200-37814200	Weak transcription	NH-A	brain
11	chr5:37812200-37814800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr5:37812200-37815000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr5:37812200-37816400	Weak transcription	HSMM	muscle
14	chr5:37812200-37822200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr5:37812400-37815200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr5:37812400-37815200	Weak transcription	Ovary	ovary
17	chr5:37812400-37816600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr5:37812400-37816800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr5:37812600-37816400	Strong transcription	Osteobl	bone
20	chr5:37812600-37816600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr5:37812800-37814200	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr5:37812800-37814800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr5:37812800-37815200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr5:37812800-37816200	Strong transcription	HSMMtube	muscle
25	chr5:37812800-37817200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr5:37813000-37816200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr5:37813000-37816400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr5:37813000-37816600	Weak transcription	Placenta	Placenta
29	chr5:37813200-37814200	Weak transcription	Colon Smooth Muscle	Colon
30	chr5:37813200-37815000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr5:37813200-37815000	Strong transcription	Fetal Intestine Small	intestine
32	chr5:37813400-37816200	Strong transcription	NHDF-Ad	bronchial
33	chr5:37813400-37824400	Weak transcription	Fetal Kidney	kidney
34	chr5:37813800-37816000	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr5:37814000-37814400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr5:37814000-37814800	Enhancers	GM12878-XiMat	blood
37	chr5:37814000-37816200	Strong transcription	Stomach Smooth Muscle	stomach
38	chr5:37814000-37816800	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr5:37814000-37817000	Enhancers	HMEC	breast

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