Variant report

Variant	rs1005930
Chromosome Location	chr18:10143877-10143878
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1005931	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4797403	0.81[EUR][1000 genomes]
rs552587	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs606280	0.94[ASN][1000 genomes]
rs624215	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv14276	chr18:10134666-10145472	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv3410028	chr18:10134811-10145112	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv909368	chr18:10142323-10272979	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1059110	chr18:10142983-10596012	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1005930	TXNDC2	cis	cerebellum	SCAN
rs1005930	CEP76	cis	cerebellum	SCAN
rs1005930	RAB31	cis	lymphoblastoid	seeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:10137400-10144400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr18:10137800-10144400	Enhancers	NHDF-Ad	bronchial
3	chr18:10138200-10144200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr18:10139800-10144400	Enhancers	Adipose Nuclei	Adipose
5	chr18:10139800-10144400	Enhancers	Fetal Lung	lung
6	chr18:10139800-10144600	Enhancers	Fetal Muscle Leg	muscle
7	chr18:10140200-10144400	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr18:10140200-10150600	Weak transcription	Spleen	Spleen
9	chr18:10140600-10150600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr18:10141200-10144000	Weak transcription	Brain Substantia Nigra	brain
11	chr18:10141400-10145400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr18:10141600-10144000	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr18:10141600-10145600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr18:10141600-10150200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr18:10141800-10144600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr18:10141800-10145400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr18:10141800-10145400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr18:10141800-10150800	Weak transcription	Right Ventricle	heart
19	chr18:10142000-10150600	Weak transcription	Gastric	stomach
20	chr18:10142400-10144400	Enhancers	Lung	lung
21	chr18:10142600-10144400	Enhancers	Ovary	ovary
22	chr18:10142800-10144400	Enhancers	Stomach Smooth Muscle	stomach
23	chr18:10142800-10145400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr18:10142800-10145400	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr18:10143000-10144000	Weak transcription	Stomach Mucosa	stomach
26	chr18:10143000-10144400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr18:10143000-10145200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr18:10143400-10144000	Weak transcription	Fetal Brain Male	brain
29	chr18:10143600-10144000	Enhancers	Fetal Heart	heart
30	chr18:10143600-10144200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr18:10143600-10144400	Enhancers	Right Atrium	heart
32	chr18:10143800-10144200	Enhancers	Brain Anterior Caudate	brain
33	chr18:10143800-10144400	Enhancers	Fetal Stomach	stomach
34	chr18:10143800-10144400	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr18:10143800-10146200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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