Variant report

Variant	rs9383865
Chromosome Location	chr6:150173179-150173180
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr6:150173172-150173622	K562	blood:	n/a	n/a
2	POLR2A	chr6:150173114-150174338	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:150164239..150168667-chr6:150168889..150173398,4	K562	blood:

Variant related genes	Relation type
ENSG00000273132	TF binding region

Extended variants
information (count: 145 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs10214845	0.85[EUR][1000 genomes]
rs10452626	0.82[EUR][1000 genomes]
rs10457850	0.82[EUR][1000 genomes]
rs10457851	0.82[EUR][1000 genomes]
rs10872651	0.84[EUR][1000 genomes]
rs10872652	0.82[EUR][1000 genomes]
rs10872653	0.81[EUR][1000 genomes]
rs10872656	0.86[EUR][1000 genomes]
rs1108889	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1112729	0.82[EUR][1000 genomes]
rs1112730	0.82[EUR][1000 genomes]
rs11155683	0.82[EUR][1000 genomes]
rs11155685	0.83[EUR][1000 genomes]
rs11155689	0.87[EUR][1000 genomes]
rs11968921	0.84[EUR][1000 genomes]
rs12175575	0.82[EUR][1000 genomes]
rs12176034	0.84[EUR][1000 genomes]
rs12179031	0.82[EUR][1000 genomes]
rs12182220	0.85[EUR][1000 genomes]
rs12210605	0.89[EUR][1000 genomes]
rs12213779	0.82[EUR][1000 genomes]
rs12525871	0.82[EUR][1000 genomes]
rs13215691	0.85[EUR][1000 genomes]
rs1413654	0.85[EUR][1000 genomes]
rs1413655	0.86[EUR][1000 genomes]
rs17672976	0.82[EUR][1000 genomes]
rs17673294	0.87[EUR][1000 genomes]
rs1889473	0.86[EUR][1000 genomes]
rs1984111	0.86[EUR][1000 genomes]
rs2095375	0.87[EUR][1000 genomes]
rs2151912	0.86[EUR][1000 genomes]
rs2151913	0.87[EUR][1000 genomes]
rs2184369	0.83[EUR][1000 genomes]
rs2184370	0.89[EUR][1000 genomes]
rs2210683	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2275045	0.89[EUR][1000 genomes]
rs2275046	0.86[EUR][1000 genomes]
rs2342764	0.89[EUR][1000 genomes]
rs2342765	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2342857	0.87[EUR][1000 genomes]
rs2342858	0.87[EUR][1000 genomes]
rs2342860	0.83[EUR][1000 genomes]
rs2342861	0.83[EUR][1000 genomes]
rs2880435	0.84[EUR][1000 genomes]
rs2880436	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3763162	0.87[EUR][1000 genomes]
rs3763163	0.87[EUR][1000 genomes]
rs3805748	0.81[EUR][1000 genomes]
rs3805749	0.82[EUR][1000 genomes]
rs3805750	0.85[EUR][1000 genomes]
rs3805751	0.85[EUR][1000 genomes]
rs3805752	0.87[EUR][1000 genomes]
rs3805753	0.85[EUR][1000 genomes]
rs3828700	0.85[EUR][1000 genomes]
rs4242279	0.89[EUR][1000 genomes]
rs4552	0.87[EUR][1000 genomes]
rs4642491	0.81[EUR][1000 genomes]
rs4816	0.85[EUR][1000 genomes]
rs4869730	0.87[EUR][1000 genomes]
rs4869731	0.87[EUR][1000 genomes]
rs4869750	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4869966	0.82[EUR][1000 genomes]
rs4870015	0.86[EUR][1000 genomes]
rs4870019	0.87[EUR][1000 genomes]
rs4870020	0.87[EUR][1000 genomes]
rs4870048	0.86[EUR][1000 genomes]
rs4870049	0.89[EUR][1000 genomes]
rs4870050	0.89[EUR][1000 genomes]
rs4870052	0.89[EUR][1000 genomes]
rs4870054	0.93[EUR][1000 genomes]
rs4870055	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55763431	0.83[EUR][1000 genomes]
rs56103941	0.89[EUR][1000 genomes]
rs56374774	0.83[EUR][1000 genomes]
rs62441303	0.82[EUR][1000 genomes]
rs62441335	0.85[EUR][1000 genomes]
rs6420132	0.86[EUR][1000 genomes]
rs6899661	0.87[EUR][1000 genomes]
rs6903998	0.86[EUR][1000 genomes]
rs6914319	0.87[EUR][1000 genomes]
rs6936395	0.87[EUR][1000 genomes]
rs7738696	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7740784	0.89[EUR][1000 genomes]
rs7743823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7744015	0.83[EUR][1000 genomes]
rs7744105	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7745915	0.86[EUR][1000 genomes]
rs7752089	0.89[EUR][1000 genomes]
rs7764846	0.87[EUR][1000 genomes]
rs7769115	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7818	0.87[EUR][1000 genomes]
rs868375	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs880245	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs880246	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9285525	0.86[EUR][1000 genomes]
rs9322218	0.82[EUR][1000 genomes]
rs9322219	0.83[EUR][1000 genomes]
rs9322220	0.85[EUR][1000 genomes]
rs9322221	0.84[EUR][1000 genomes]
rs9322223	0.86[EUR][1000 genomes]
rs9322224	0.86[EUR][1000 genomes]
rs933055	0.87[EUR][1000 genomes]
rs9371199	0.89[EUR][1000 genomes]
rs9371201	0.84[EUR][1000 genomes]
rs9371207	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9371486	0.85[EUR][1000 genomes]
rs9372044	0.83[EUR][1000 genomes]
rs9383546	0.86[EUR][1000 genomes]
rs9383843	0.81[EUR][1000 genomes]
rs9383864	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9383874	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9397022	0.87[EUR][1000 genomes]
rs9397036	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9397357	0.87[EUR][1000 genomes]
rs9478848	0.86[EUR][1000 genomes]
rs9505972	0.84[EUR][1000 genomes]
rs9505974	0.82[EUR][1000 genomes]
rs952165	0.86[EUR][1000 genomes]
rs952166	0.86[EUR][1000 genomes]
rs958953	0.83[EUR][1000 genomes]
rs9688412	0.86[EUR][1000 genomes]
rs9688803	0.88[EUR][1000 genomes]
rs9688809	0.88[EUR][1000 genomes]
rs9688867	0.81[EUR][1000 genomes]
rs9688897	0.87[EUR][1000 genomes]
rs9688902	0.88[EUR][1000 genomes]
rs9688938	0.88[EUR][1000 genomes]
rs9688940	0.88[EUR][1000 genomes]
rs9689025	0.85[EUR][1000 genomes]
rs9689036	0.82[EUR][1000 genomes]
rs9689242	0.88[EUR][1000 genomes]
rs9689269	0.85[EUR][1000 genomes]
rs9689447	0.86[EUR][1000 genomes]
rs9765929	0.82[EUR][1000 genomes]
rs9765965	0.81[EUR][1000 genomes]
rs9766214	0.81[EUR][1000 genomes]
rs9766444	0.81[EUR][1000 genomes]
rs9766525	0.85[EUR][1000 genomes]
rs9766562	0.87[EUR][1000 genomes]
rs9767077	0.88[EUR][1000 genomes]
rs9767122	0.85[EUR][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	nsv886762	chr6:149866452-150174507	Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv886763	chr6:150091219-150174507	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv886764	chr6:150114745-150393683	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv517022	chr6:150145001-150426272	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs9383865	GINM1	cis	Whole Blood	GTEx
rs9383865	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx
rs9383865	RP11-350J20.5	cis	lung	GTEx
rs9383865	RP11-350J20.5	cis	Esophagus Mucosa	GTEx
rs9383865	NUP43	Cis_1M	lymphoblastoid	RTeQTL
rs9383865	RAET1G	cis	Thyroid	GTEx
rs9383865	RP11-350J20.5	cis	Esophagus Muscularis	GTEx
rs9383865	LRP11	cis	Skin Sun Exposed Lower leg	GTEx
rs9383865	RP11-350J20.5	cis	Artery Tibial	GTEx
rs9383865	C6orf72	Cis_1M	lymphoblastoid	RTeQTL
rs9383865	RP11-350J20.9	cis	Esophagus Mucosa	GTEx
rs9383865	RP11-350J20.5	cis	Thyroid	GTEx
rs9383865	RP11-350J20.5	cis	Adipose Subcutaneous	GTEx
rs9383865	NUP43	cis	Whole Blood	GTEx
rs9383865	RP11-350J20.5	cis	Nerve Tibial	GTEx

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150073800-150182400	Weak transcription	Fetal Brain Male	brain
2	chr6:150105800-150176400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:150155800-150182600	Weak transcription	Dnd41	blood
4	chr6:150158800-150176400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:150162200-150175800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:150162600-150177200	Weak transcription	Fetal Lung	lung
7	chr6:150163600-150175800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:150164400-150181800	Weak transcription	Brain Germinal Matrix	brain
9	chr6:150165000-150181800	Weak transcription	Fetal Brain Female	brain
10	chr6:150167800-150181400	Weak transcription	Right Atrium	heart
11	chr6:150168600-150173400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr6:150168600-150173600	Weak transcription	Esophagus	oesophagus
13	chr6:150168600-150175200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:150168600-150175200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:150168600-150175200	Weak transcription	Pancreas	Pancrea
16	chr6:150168800-150173200	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr6:150168800-150173400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr6:150168800-150175800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr6:150168800-150182600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr6:150168800-150183400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr6:150169000-150175200	Weak transcription	Gastric	stomach
22	chr6:150169000-150181200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr6:150169200-150177800	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr6:150169200-150183000	Weak transcription	Brain Substantia Nigra	brain
25	chr6:150169400-150173600	Weak transcription	Stomach Mucosa	stomach
26	chr6:150169400-150175800	Weak transcription	Fetal Intestine Large	intestine
27	chr6:150169400-150175800	Weak transcription	HSMMtube	muscle
28	chr6:150169400-150176000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr6:150169400-150176000	Weak transcription	Colon Smooth Muscle	Colon
30	chr6:150169400-150183200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr6:150169600-150173200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr6:150169600-150174200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr6:150170200-150173400	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr6:150171000-150173200	Strong transcription	HepG2	liver
35	chr6:150171000-150174200	Strong transcription	Stomach Smooth Muscle	stomach
36	chr6:150171000-150174400	Strong transcription	Fetal Muscle Leg	muscle
37	chr6:150171200-150174200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr6:150171200-150174400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr6:150171400-150174000	Strong transcription	Brain Anterior Caudate	brain
40	chr6:150171800-150174200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:150172000-150173200	Strong transcription	Ovary	ovary
42	chr6:150172000-150173600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr6:150172000-150173600	Genic enhancers	A549	lung
44	chr6:150172000-150174200	Strong transcription	Adipose Nuclei	Adipose
45	chr6:150172000-150174200	Strong transcription	Duodenum Mucosa	Duodenum
46	chr6:150172000-150174200	Strong transcription	Fetal Stomach	stomach
47	chr6:150172000-150174200	Genic enhancers	NHDF-Ad	bronchial
48	chr6:150172200-150173600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr6:150172200-150173800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr6:150172200-150173800	Strong transcription	Brain Hippocampus Middle	brain

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