Variant report

Variant	rs9383874
Chromosome Location	chr6:150179559-150179560
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	chr6:150179152..150182085-chr6:150183567..150186246,3	K562	blood:
2	chr6:150166110..150169897-chr6:150177295..150181208,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000268592	Chromatin interaction
ENSG00000120256	Chromatin interaction

Extended variants
information (count: 143 )
Associated
traits (count: 14 )

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

rs_ID	r²[population]
rs10214845	0.84[EUR][1000 genomes]
rs10452626	0.81[EUR][1000 genomes]
rs10457850	0.81[EUR][1000 genomes]
rs10457851	0.81[EUR][1000 genomes]
rs10872651	0.84[EUR][1000 genomes]
rs10872652	0.81[EUR][1000 genomes]
rs10872653	0.81[EUR][1000 genomes]
rs10872656	0.86[EUR][1000 genomes]
rs1108889	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1112729	0.81[EUR][1000 genomes]
rs1112730	0.81[EUR][1000 genomes]
rs11155683	0.82[EUR][1000 genomes]
rs11155685	0.82[EUR][1000 genomes]
rs11155689	0.87[EUR][1000 genomes]
rs11968921	0.84[EUR][1000 genomes]
rs12175575	0.81[EUR][1000 genomes]
rs12176034	0.84[EUR][1000 genomes]
rs12179031	0.81[EUR][1000 genomes]
rs12182220	0.84[EUR][1000 genomes]
rs12210605	0.90[EUR][1000 genomes]
rs12213779	0.81[EUR][1000 genomes]
rs12525871	0.81[EUR][1000 genomes]
rs13215691	0.84[EUR][1000 genomes]
rs1413654	0.84[EUR][1000 genomes]
rs1413655	0.86[EUR][1000 genomes]
rs17672976	0.81[EUR][1000 genomes]
rs17673294	0.86[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	0.82[EUR][1000 genomes]
rs2184370	0.90[EUR][1000 genomes]
rs2210683	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2275045	0.90[EUR][1000 genomes]
rs2275046	0.86[EUR][1000 genomes]
rs2342764	0.90[EUR][1000 genomes]
rs2342765	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2342857	0.87[EUR][1000 genomes]
rs2342858	0.87[EUR][1000 genomes]
rs2342860	0.82[EUR][1000 genomes]
rs2342861	0.82[EUR][1000 genomes]
rs2880435	0.83[EUR][1000 genomes]
rs2880436	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	0.83[EUR][1000 genomes]
rs3805750	0.84[EUR][1000 genomes]
rs3805751	0.84[EUR][1000 genomes]
rs3805752	0.88[EUR][1000 genomes]
rs3805753	0.84[EUR][1000 genomes]
rs3828700	0.84[EUR][1000 genomes]
rs4242279	0.90[EUR][1000 genomes]
rs4552	0.87[EUR][1000 genomes]
rs4642491	0.80[EUR][1000 genomes]
rs4816	0.84[EUR][1000 genomes]
rs4869730	0.87[EUR][1000 genomes]
rs4869731	0.87[EUR][1000 genomes]
rs4869750	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4869966	0.81[EUR][1000 genomes]
rs4870015	0.86[EUR][1000 genomes]
rs4870019	0.86[EUR][1000 genomes]
rs4870020	0.86[EUR][1000 genomes]
rs4870048	0.85[EUR][1000 genomes]
rs4870049	0.90[EUR][1000 genomes]
rs4870050	0.89[EUR][1000 genomes]
rs4870052	0.90[EUR][1000 genomes]
rs4870054	0.93[EUR][1000 genomes]
rs4870055	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55763431	0.82[EUR][1000 genomes]
rs56103941	0.90[EUR][1000 genomes]
rs56374774	0.82[EUR][1000 genomes]
rs62441303	0.81[EUR][1000 genomes]
rs62441335	0.84[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	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7740784	0.90[EUR][1000 genomes]
rs7743823	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7744015	0.82[EUR][1000 genomes]
rs7744105	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7745915	0.86[EUR][1000 genomes]
rs7752089	0.90[EUR][1000 genomes]
rs7764846	0.86[EUR][1000 genomes]
rs7769115	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7818	0.86[EUR][1000 genomes]
rs868375	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs880245	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs880246	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9285525	0.86[EUR][1000 genomes]
rs9322218	0.81[EUR][1000 genomes]
rs9322219	0.82[EUR][1000 genomes]
rs9322220	0.84[EUR][1000 genomes]
rs9322221	0.84[EUR][1000 genomes]
rs9322223	0.86[EUR][1000 genomes]
rs9322224	0.85[EUR][1000 genomes]
rs933055	0.87[EUR][1000 genomes]
rs9371199	0.90[EUR][1000 genomes]
rs9371201	0.84[EUR][1000 genomes]
rs9371207	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9371486	0.85[EUR][1000 genomes]
rs9372044	0.82[EUR][1000 genomes]
rs9383546	0.86[EUR][1000 genomes]
rs9383843	0.81[EUR][1000 genomes]
rs9383864	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9383865	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9397022	0.87[EUR][1000 genomes]
rs9397036	0.91[AMR][1000 genomes];0.99[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	0.81[EUR][1000 genomes]
rs952165	0.86[EUR][1000 genomes]
rs952166	0.86[EUR][1000 genomes]
rs958953	0.84[EUR][1000 genomes]
rs9688412	0.86[EUR][1000 genomes]
rs9688803	0.87[EUR][1000 genomes]
rs9688809	0.88[EUR][1000 genomes]
rs9688867	0.80[EUR][1000 genomes]
rs9688897	0.86[EUR][1000 genomes]
rs9688902	0.87[EUR][1000 genomes]
rs9688938	0.88[EUR][1000 genomes]
rs9688940	0.88[EUR][1000 genomes]
rs9689025	0.85[EUR][1000 genomes]
rs9689036	0.81[EUR][1000 genomes]
rs9689242	0.88[EUR][1000 genomes]
rs9689269	0.84[EUR][1000 genomes]
rs9689447	0.86[EUR][1000 genomes]
rs9765929	0.81[EUR][1000 genomes]
rs9765965	0.81[EUR][1000 genomes]
rs9766214	0.81[EUR][1000 genomes]
rs9766444	0.81[EUR][1000 genomes]
rs9766525	0.84[EUR][1000 genomes]
rs9766562	0.87[EUR][1000 genomes]
rs9767077	0.87[EUR][1000 genomes]
rs9767122	0.84[EUR][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	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
2	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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs9383874	RP11-350J20.5	cis	Esophagus Muscularis	GTEx
rs9383874	NUP43	Cis_1M	lymphoblastoid	RTeQTL
rs9383874	C6orf72	Cis_1M	lymphoblastoid	RTeQTL
rs9383874	NUP43	cis	Whole Blood	GTEx
rs9383874	LRP11	cis	Skin Sun Exposed Lower leg	GTEx
rs9383874	GINM1	cis	Whole Blood	GTEx
rs9383874	RP11-350J20.5	cis	lung	GTEx
rs9383874	RP11-350J20.5	cis	Thyroid	GTEx
rs9383874	RP11-350J20.5	cis	Adipose Subcutaneous	GTEx
rs9383874	RP11-350J20.9	cis	Esophagus Mucosa	GTEx
rs9383874	RAET1G	cis	Thyroid	GTEx
rs9383874	RP11-350J20.5	cis	Artery Tibial	GTEx
rs9383874	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx
rs9383874	RP11-350J20.5	cis	Esophagus Mucosa	GTEx

Chromatin state (count:81 , 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	chr6:150155800-150182600	Weak transcription	Dnd41	blood
3	chr6:150164400-150181800	Weak transcription	Brain Germinal Matrix	brain
4	chr6:150165000-150181800	Weak transcription	Fetal Brain Female	brain
5	chr6:150167800-150181400	Weak transcription	Right Atrium	heart
6	chr6:150168800-150182600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:150168800-150183400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr6:150169000-150181200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:150169200-150183000	Weak transcription	Brain Substantia Nigra	brain
10	chr6:150169400-150183200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr6:150172600-150181600	Weak transcription	Brain Angular Gyrus	brain
12	chr6:150173000-150181200	Weak transcription	Liver	Liver
13	chr6:150173000-150181600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr6:150173000-150184200	Weak transcription	Aorta	Aorta
15	chr6:150173200-150183200	Weak transcription	Ovary	ovary
16	chr6:150173800-150181800	Weak transcription	Brain Hippocampus Middle	brain
17	chr6:150174000-150181600	Weak transcription	Brain Anterior Caudate	brain
18	chr6:150174200-150181600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr6:150174200-150181600	Weak transcription	Fetal Stomach	stomach
20	chr6:150174200-150181800	Weak transcription	Adipose Nuclei	Adipose
21	chr6:150174200-150182600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr6:150176000-150181800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr6:150176200-150181200	Weak transcription	Esophagus	oesophagus
24	chr6:150176200-150183200	Weak transcription	Fetal Intestine Large	intestine
25	chr6:150176400-150182000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr6:150176600-150180600	Weak transcription	Gastric	stomach
27	chr6:150176600-150181400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr6:150176600-150182400	Weak transcription	Fetal Intestine Small	intestine
29	chr6:150176600-150183200	Weak transcription	Colon Smooth Muscle	Colon
30	chr6:150176600-150183400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr6:150176800-150180600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr6:150176800-150181200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr6:150176800-150181400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr6:150176800-150181600	Weak transcription	Lung	lung
35	chr6:150176800-150182200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr6:150176800-150183400	Weak transcription	HSMMtube	muscle
37	chr6:150177200-150180200	Weak transcription	Stomach Mucosa	stomach
38	chr6:150177200-150180800	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr6:150177200-150181200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr6:150177200-150181200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr6:150177200-150181200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr6:150177200-150182000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr6:150177200-150183000	Weak transcription	Fetal Kidney	kidney
44	chr6:150177600-150180800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr6:150177600-150183000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr6:150177600-150183200	Weak transcription	Fetal Lung	lung
47	chr6:150177800-150179800	Weak transcription	HepG2	liver
48	chr6:150178000-150179800	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr6:150178000-150180600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr6:150178000-150183200	Weak transcription	H9 Cell Line	embryonic stem cell

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