Variant report

Variant	rs7041687
Chromosome Location	chr9:86464195-86464196
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10868069	0.90[AMR][1000 genomes]
rs10868072	0.84[AMR][1000 genomes]
rs11140284	0.82[AMR][1000 genomes]
rs11999592	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12001505	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12001918	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12003101	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12003500	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12552069	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12554775	0.80[ASN][1000 genomes]
rs17064724	0.80[ASN][1000 genomes]
rs2184086	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2990912	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2990915	0.94[AFR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34690696	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35784768	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55654273	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55872219	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56055736	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57267691	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57531526	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57957686	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58248061	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58474042	0.80[EUR][1000 genomes]
rs59158043	0.80[ASN][1000 genomes]
rs59474223	0.80[ASN][1000 genomes]
rs60277614	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60349318	0.80[ASN][1000 genomes]
rs61490202	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62561948	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7021609	0.80[ASN][1000 genomes]
rs7036293	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7038235	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7040164	0.80[ASN][1000 genomes]
rs7040843	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7042053	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7046229	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7048626	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73463303	0.80[ASN][1000 genomes]
rs73463313	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73463327	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73463379	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73463395	0.80[EUR][1000 genomes]
rs7849708	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7850288	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7850404	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7856614	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7857619	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7859830	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7859928	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7864058	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7874481	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9695726	0.93[AMR][1000 genomes]
rs970846	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
8	esv3440485	chr9:86461957-86464705	Weak transcription Strong transcription Active TSS ZNF genes & repeats	TF binding region lncRNA	1 gene(s)	inside rSNPs	n/a
9	esv3443435	chr9:86462182-86464480	Strong transcription Weak transcription Active TSS	TF binding region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7041687	C4orf31	trans	lymphoblastoid	RTeQTL

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86447800-86470800	Weak transcription	Brain Germinal Matrix	brain
2	chr9:86452000-86467800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr9:86456200-86466200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr9:86456600-86472600	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr9:86457400-86464200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr9:86457400-86468400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr9:86457400-86469000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr9:86459800-86464200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr9:86459800-86466400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr9:86460000-86474000	Weak transcription	Adipose Nuclei	Adipose
11	chr9:86460400-86465400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr9:86460600-86465400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr9:86460600-86518200	Weak transcription	Thymus	Thymus
14	chr9:86461600-86535400	Weak transcription	Fetal Intestine Small	intestine
15	chr9:86461600-86535400	Weak transcription	Ovary	ovary
16	chr9:86462200-86466400	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr9:86462200-86471200	Weak transcription	Liver	Liver
18	chr9:86462200-86475400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:86462200-86535200	Weak transcription	Fetal Brain Female	brain
20	chr9:86462400-86464400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr9:86462400-86482400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr9:86462600-86464200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr9:86462600-86464200	Weak transcription	Brain Angular Gyrus	brain
24	chr9:86462600-86464200	Weak transcription	Duodenum Mucosa	Duodenum
25	chr9:86462600-86464200	Weak transcription	Gastric	stomach
26	chr9:86462600-86464600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr9:86462600-86468600	Weak transcription	Primary T cells from cord blood	blood
28	chr9:86462600-86469600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr9:86462600-86499200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr9:86462600-86500600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr9:86462600-86503800	Weak transcription	Dnd41	blood
32	chr9:86462600-86535200	Weak transcription	Brain Anterior Caudate	brain
33	chr9:86462800-86464400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr9:86462800-86465400	Weak transcription	Fetal Thymus	thymus
35	chr9:86462800-86468600	Weak transcription	Placenta	Placenta
36	chr9:86462800-86471200	Weak transcription	Fetal Lung	lung
37	chr9:86462800-86515000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr9:86462800-86518000	Weak transcription	Fetal Intestine Large	intestine
39	chr9:86462800-86518000	Weak transcription	Fetal Stomach	stomach

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