Variant report

Variant	rs2990912
Chromosome Location	chr9:86460128-86460129
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10868069	0.81[AMR][1000 genomes]
rs12001918	0.81[AMR][1000 genomes]
rs12552069	0.81[AMR][1000 genomes]
rs12554775	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17064724	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2184086	0.81[AMR][1000 genomes]
rs2990915	0.80[AFR][1000 genomes]
rs55654273	0.80[ASN][1000 genomes]
rs55872219	0.81[AMR][1000 genomes]
rs59158043	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59474223	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60349318	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61491479	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62561948	0.80[ASN][1000 genomes]
rs7021609	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7036293	0.80[AFR][1000 genomes]
rs7039941	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7040164	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7041687	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7042053	0.80[ASN][1000 genomes]
rs7045525	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73463303	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73463313	0.80[ASN][1000 genomes]
rs73463379	0.81[AMR][1000 genomes]
rs7856614	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7857619	0.81[AMR][1000 genomes]
rs7859830	0.81[AMR][1000 genomes]
rs7864058	0.80[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	nsv469859	chr9:86398152-86587957	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv482641	chr9:86398152-86587957	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	esv2758192	chr9:86414024-86603602	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2759701	chr9:86414024-86603602	Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active 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 miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv982312	chr9:86424154-86490046	Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv6590	chr9:86435603-86480442	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv8540	chr9:86458587-86470369	Strong transcription ZNF genes & repeats Weak transcription Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2990912	C4orf31	trans	lymphoblastoid	RTeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86447800-86461200	Weak transcription	Fetal Brain Female	brain
2	chr9:86447800-86470800	Weak transcription	Brain Germinal Matrix	brain
3	chr9:86452000-86467800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr9:86452200-86464000	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr9:86453400-86461200	Weak transcription	Fetal Intestine Large	intestine
6	chr9:86454400-86461200	Weak transcription	Primary T cells from cord blood	blood
7	chr9:86455400-86461200	Weak transcription	Dnd41	blood
8	chr9:86455400-86461400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr9:86456000-86461000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr9:86456000-86463600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr9:86456200-86466200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:86456600-86472600	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr9:86456800-86463200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr9:86457000-86464000	Weak transcription	Left Ventricle	heart
15	chr9:86457400-86461000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr9:86457400-86461200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr9:86457400-86461200	Weak transcription	Brain Anterior Caudate	brain
18	chr9:86457400-86461200	Weak transcription	Fetal Lung	lung
19	chr9:86457400-86461200	Weak transcription	Fetal Muscle Leg	muscle
20	chr9:86457400-86461200	Weak transcription	Lung	lung
21	chr9:86457400-86461400	Weak transcription	Fetal Thymus	thymus
22	chr9:86457400-86461600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr9:86457400-86461800	Weak transcription	Fetal Brain Male	brain
24	chr9:86457400-86464200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr9:86457400-86468400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr9:86457400-86469000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr9:86457600-86464000	Weak transcription	Pancreas	Pancrea
28	chr9:86458000-86463600	Weak transcription	Esophagus	oesophagus
29	chr9:86458600-86462800	Strong transcription	Fetal Stomach	stomach
30	chr9:86459000-86460800	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr9:86459000-86461200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr9:86459200-86460800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr9:86459400-86461000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr9:86459400-86461000	Weak transcription	Fetal Intestine Small	intestine
35	chr9:86459400-86461200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr9:86459400-86461200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr9:86459400-86461200	Weak transcription	Liver	Liver
38	chr9:86459400-86461200	Weak transcription	Gastric	stomach
39	chr9:86459600-86461200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr9:86459600-86461200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr9:86459600-86461200	Weak transcription	Brain Angular Gyrus	brain
42	chr9:86459600-86461200	Weak transcription	Duodenum Mucosa	Duodenum
43	chr9:86459600-86461200	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr9:86459600-86461200	Weak transcription	Fetal Kidney	kidney
45	chr9:86459600-86461200	Weak transcription	Placenta	Placenta
46	chr9:86459600-86461200	Weak transcription	Ovary	ovary
47	chr9:86459600-86461200	Weak transcription	Spleen	Spleen
48	chr9:86459600-86464000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr9:86459800-86461400	Weak transcription	Fetal Muscle Trunk	muscle
50	chr9:86459800-86464200	Weak transcription	Brain Inferior Temporal Lobe	brain

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