Variant report

Variant	rs9371486
Chromosome Location	chr6:150153226-150153227
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:150151705..150153570-chr6:150183035..150185955,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000120256	Chromatin interaction
ENSG00000268592	Chromatin interaction

Extended variants
information (count: 279 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:274)

rs_ID	r²[population]
rs10214845	0.90[EUR][1000 genomes]
rs10452626	0.87[EUR][1000 genomes]
rs10457850	0.87[EUR][1000 genomes]
rs10457851	0.87[EUR][1000 genomes]
rs10747276	0.84[EUR][1000 genomes]
rs10782314	0.83[EUR][1000 genomes]
rs10782315	0.82[EUR][1000 genomes]
rs10782316	0.84[EUR][1000 genomes]
rs10782317	0.84[EUR][1000 genomes]
rs10782318	0.84[EUR][1000 genomes]
rs10872643	0.81[EUR][1000 genomes]
rs10872644	0.83[EUR][1000 genomes]
rs10872646	0.84[EUR][1000 genomes]
rs10872647	0.87[EUR][1000 genomes]
rs10872648	0.87[EUR][1000 genomes]
rs10872649	0.84[EUR][1000 genomes]
rs10872650	0.84[EUR][1000 genomes]
rs10872651	0.90[EUR][1000 genomes]
rs10872652	0.87[EUR][1000 genomes]
rs10872653	0.86[EUR][1000 genomes]
rs10872656	0.91[EUR][1000 genomes]
rs1108889	0.85[EUR][1000 genomes]
rs1112729	0.87[EUR][1000 genomes]
rs1112730	0.87[EUR][1000 genomes]
rs11155669	0.80[EUR][1000 genomes]
rs11155671	0.82[EUR][1000 genomes]
rs11155674	0.81[EUR][1000 genomes]
rs11155675	0.86[EUR][1000 genomes]
rs11155676	0.80[EUR][1000 genomes]
rs11155677	0.83[EUR][1000 genomes]
rs11155679	0.87[EUR][1000 genomes]
rs11155680	0.84[EUR][1000 genomes]
rs11155681	0.80[EUR][1000 genomes]
rs11155682	0.82[EUR][1000 genomes]
rs11155683	0.87[EUR][1000 genomes]
rs11155685	0.88[EUR][1000 genomes]
rs11155689	0.92[EUR][1000 genomes]
rs1125	0.84[EUR][1000 genomes]
rs11968921	0.90[EUR][1000 genomes]
rs12111376	0.83[EUR][1000 genomes]
rs12174349	0.82[EUR][1000 genomes]
rs12174716	0.82[EUR][1000 genomes]
rs12175575	0.87[EUR][1000 genomes]
rs12176034	0.89[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12178310	0.82[EUR][1000 genomes]
rs12179031	0.87[EUR][1000 genomes]
rs12182220	0.90[EUR][1000 genomes]
rs12183664	0.80[EUR][1000 genomes]
rs12191643	0.80[EUR][1000 genomes]
rs12200670	0.81[EUR][1000 genomes]
rs12203703	0.82[EUR][1000 genomes]
rs12205092	0.84[EUR][1000 genomes]
rs12206402	0.81[EUR][1000 genomes]
rs12210605	0.95[EUR][1000 genomes]
rs12211511	0.80[EUR][1000 genomes]
rs12213779	0.87[EUR][1000 genomes]
rs12525871	0.87[EUR][1000 genomes]
rs12526675	0.83[EUR][1000 genomes]
rs12528279	0.84[EUR][1000 genomes]
rs12529698	0.82[EUR][1000 genomes]
rs12660304	0.83[EUR][1000 genomes]
rs12662174	0.80[EUR][1000 genomes]
rs13215691	0.90[EUR][1000 genomes]
rs1413654	0.90[EUR][1000 genomes]
rs1413655	0.91[EUR][1000 genomes]
rs17672976	0.87[EUR][1000 genomes]
rs17673294	0.92[EUR][1000 genomes]
rs1889473	0.91[EUR][1000 genomes]
rs1934534	0.81[EUR][1000 genomes]
rs1984111	0.91[EUR][1000 genomes]
rs2065663	0.84[EUR][1000 genomes]
rs2095375	0.92[EUR][1000 genomes]
rs2151909	0.85[EUR][1000 genomes]
rs2151912	0.91[EUR][1000 genomes]
rs2151913	0.92[EUR][1000 genomes]
rs2184369	0.88[EUR][1000 genomes]
rs2184370	0.95[EUR][1000 genomes]
rs2185352	0.81[EUR][1000 genomes]
rs2210683	0.82[EUR][1000 genomes]
rs2275045	0.95[EUR][1000 genomes]
rs2275046	0.91[EUR][1000 genomes]
rs2297928	0.82[EUR][1000 genomes]
rs2297930	0.82[EUR][1000 genomes]
rs2297932	0.82[EUR][1000 genomes]
rs2342764	0.95[EUR][1000 genomes]
rs2342765	0.82[EUR][1000 genomes]
rs2342857	0.92[EUR][1000 genomes]
rs2342858	0.92[EUR][1000 genomes]
rs2342860	0.88[EUR][1000 genomes]
rs2342861	0.88[EUR][1000 genomes]
rs2880435	0.89[EUR][1000 genomes]
rs2880436	0.85[EUR][1000 genomes]
rs34157004	0.81[EUR][1000 genomes]
rs35830138	0.81[EUR][1000 genomes]
rs35961297	0.81[EUR][1000 genomes]
rs35967444	0.81[EUR][1000 genomes]
rs3763161	0.85[EUR][1000 genomes]
rs3763162	0.92[EUR][1000 genomes]
rs3763163	0.92[EUR][1000 genomes]
rs3798761	0.81[EUR][1000 genomes]
rs3805748	0.86[EUR][1000 genomes]
rs3805749	0.88[EUR][1000 genomes]
rs3805750	0.90[EUR][1000 genomes]
rs3805751	0.90[EUR][1000 genomes]
rs3805752	0.93[EUR][1000 genomes]
rs3805753	0.90[EUR][1000 genomes]
rs3828700	0.90[EUR][1000 genomes]
rs3924871	0.81[EUR][1000 genomes]
rs4242279	0.95[EUR][1000 genomes]
rs4354168	0.81[EUR][1000 genomes]
rs4380763	0.81[EUR][1000 genomes]
rs4421206	0.81[EUR][1000 genomes]
rs4455682	0.81[EUR][1000 genomes]
rs4552	0.92[EUR][1000 genomes]
rs4642491	0.86[EUR][1000 genomes]
rs4816	0.90[EUR][1000 genomes]
rs4869730	0.92[EUR][1000 genomes]
rs4869731	0.92[EUR][1000 genomes]
rs4869750	0.82[EUR][1000 genomes]
rs4869812	0.81[EUR][1000 genomes]
rs4869966	0.87[EUR][1000 genomes]
rs4870015	0.91[EUR][1000 genomes]
rs4870019	0.92[EUR][1000 genomes]
rs4870020	0.92[EUR][1000 genomes]
rs4870048	0.91[EUR][1000 genomes]
rs4870049	0.95[EUR][1000 genomes]
rs4870050	0.95[EUR][1000 genomes]
rs4870052	0.95[EUR][1000 genomes]
rs4870054	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4870055	0.81[EUR][1000 genomes]
rs4870267	0.81[EUR][1000 genomes]
rs4870388	0.81[EUR][1000 genomes]
rs4870493	0.81[EUR][1000 genomes]
rs4870509	0.81[EUR][1000 genomes]
rs4870529	0.82[EUR][1000 genomes]
rs55763431	0.88[EUR][1000 genomes]
rs55849538	0.81[EUR][1000 genomes]
rs55938765	0.84[EUR][1000 genomes]
rs56091542	0.81[EUR][1000 genomes]
rs56103941	0.95[EUR][1000 genomes]
rs56374774	0.88[EUR][1000 genomes]
rs56397000	0.83[EUR][1000 genomes]
rs57938011	0.81[EUR][1000 genomes]
rs60424881	0.83[EUR][1000 genomes]
rs62439811	0.81[EUR][1000 genomes]
rs62439837	0.81[EUR][1000 genomes]
rs62439840	0.81[EUR][1000 genomes]
rs62439842	0.81[EUR][1000 genomes]
rs62441279	0.82[EUR][1000 genomes]
rs62441284	0.84[EUR][1000 genomes]
rs62441303	0.87[EUR][1000 genomes]
rs62441335	0.90[EUR][1000 genomes]
rs6420132	0.91[EUR][1000 genomes]
rs66516768	0.81[EUR][1000 genomes]
rs6899661	0.92[EUR][1000 genomes]
rs6903998	0.91[EUR][1000 genomes]
rs6913486	0.81[EUR][1000 genomes]
rs6914319	0.92[EUR][1000 genomes]
rs6936395	0.92[EUR][1000 genomes]
rs7450246	0.81[EUR][1000 genomes]
rs7738696	0.85[EUR][1000 genomes]
rs7740278	0.81[EUR][1000 genomes]
rs7740784	0.95[EUR][1000 genomes]
rs7743823	0.85[EUR][1000 genomes]
rs7744015	0.88[EUR][1000 genomes]
rs7744105	0.85[EUR][1000 genomes]
rs7745915	0.91[EUR][1000 genomes]
rs7752089	0.95[EUR][1000 genomes]
rs7752594	0.81[EUR][1000 genomes]
rs7754399	0.81[EUR][1000 genomes]
rs7764846	0.92[EUR][1000 genomes]
rs7767622	0.81[EUR][1000 genomes]
rs7769115	0.85[EUR][1000 genomes]
rs7818	0.92[EUR][1000 genomes]
rs868375	0.83[EUR][1000 genomes]
rs880245	0.85[EUR][1000 genomes]
rs880246	0.85[EUR][1000 genomes]
rs9285522	0.81[EUR][1000 genomes]
rs9285525	0.91[EUR][1000 genomes]
rs9322204	0.81[EUR][1000 genomes]
rs9322207	0.81[EUR][1000 genomes]
rs9322208	0.81[EUR][1000 genomes]
rs9322209	0.81[EUR][1000 genomes]
rs9322210	0.81[EUR][1000 genomes]
rs9322214	0.81[EUR][1000 genomes]
rs9322215	0.80[EUR][1000 genomes]
rs9322218	0.87[EUR][1000 genomes]
rs9322219	0.88[EUR][1000 genomes]
rs9322220	0.90[EUR][1000 genomes]
rs9322221	0.89[EUR][1000 genomes]
rs9322223	0.91[EUR][1000 genomes]
rs9322224	0.91[EUR][1000 genomes]
rs933055	0.92[EUR][1000 genomes]
rs9371199	0.95[EUR][1000 genomes]
rs9371201	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9371207	0.85[EUR][1000 genomes]
rs9372044	0.88[EUR][1000 genomes]
rs9383546	0.91[EUR][1000 genomes]
rs9383812	0.81[EUR][1000 genomes]
rs9383843	0.87[EUR][1000 genomes]
rs9383844	0.82[EUR][1000 genomes]
rs9383864	0.85[EUR][1000 genomes]
rs9383865	0.85[EUR][1000 genomes]
rs9383874	0.85[EUR][1000 genomes]
rs9393132	0.81[EUR][1000 genomes]
rs9393175	0.81[EUR][1000 genomes]
rs9397022	0.92[EUR][1000 genomes]
rs9397036	0.85[EUR][1000 genomes]
rs9397357	0.92[EUR][1000 genomes]
rs9406286	0.81[EUR][1000 genomes]
rs9478291	0.83[EUR][1000 genomes]
rs9478848	0.91[EUR][1000 genomes]
rs9479094	0.82[EUR][1000 genomes]
rs9479494	0.83[EUR][1000 genomes]
rs9479810	0.81[EUR][1000 genomes]
rs9480009	0.84[EUR][1000 genomes]
rs9480031	0.84[EUR][1000 genomes]
rs9505823	0.80[EUR][1000 genomes]
rs9505967	0.81[EUR][1000 genomes]
rs9505972	0.90[EUR][1000 genomes]
rs9505974	0.87[EUR][1000 genomes]
rs9505975	0.84[EUR][1000 genomes]
rs952165	0.91[EUR][1000 genomes]
rs952166	0.91[EUR][1000 genomes]
rs958953	0.89[EUR][1000 genomes]
rs9688350	0.83[EUR][1000 genomes]
rs9688412	0.91[EUR][1000 genomes]
rs9688452	0.81[EUR][1000 genomes]
rs9688517	0.83[EUR][1000 genomes]
rs9688699	0.83[EUR][1000 genomes]
rs9688794	0.80[EUR][1000 genomes]
rs9688803	0.93[EUR][1000 genomes]
rs9688809	0.93[EUR][1000 genomes]
rs9688861	0.81[EUR][1000 genomes]
rs9688867	0.85[EUR][1000 genomes]
rs9688897	0.93[EUR][1000 genomes]
rs9688902	0.93[EUR][1000 genomes]
rs9688938	0.93[EUR][1000 genomes]
rs9688940	0.93[EUR][1000 genomes]
rs9689025	0.90[EUR][1000 genomes]
rs9689036	0.87[EUR][1000 genomes]
rs9689084	0.81[EUR][1000 genomes]
rs9689242	0.93[EUR][1000 genomes]
rs9689269	0.90[EUR][1000 genomes]
rs9689340	0.83[EUR][1000 genomes]
rs9689447	0.91[EUR][1000 genomes]
rs9689599	0.80[EUR][1000 genomes]
rs9689694	0.84[EUR][1000 genomes]
rs9689702	0.83[EUR][1000 genomes]
rs9765861	0.82[EUR][1000 genomes]
rs9765929	0.87[EUR][1000 genomes]
rs9765965	0.86[EUR][1000 genomes]
rs9766004	0.84[EUR][1000 genomes]
rs9766214	0.86[EUR][1000 genomes]
rs9766444	0.86[EUR][1000 genomes]
rs9766525	0.90[EUR][1000 genomes]
rs9766562	0.92[EUR][1000 genomes]
rs9766886	0.81[EUR][1000 genomes]
rs9767077	0.93[EUR][1000 genomes]
rs9767105	0.80[EUR][1000 genomes]
rs9767113	0.82[EUR][1000 genomes]
rs9767122	0.90[EUR][1000 genomes]
rs9767123	0.81[EUR][1000 genomes]
rs9767192	0.80[EUR][1000 genomes]
rs9767309	0.82[EUR][1000 genomes]
rs9767652	0.83[EUR][1000 genomes]
rs9767727	0.81[EUR][1000 genomes]
rs9800580	0.80[EUR][1000 genomes]
rs9800603	0.80[EUR][1000 genomes]
rs9800614	0.82[EUR][1000 genomes]
rs9800736	0.81[EUR][1000 genomes]
rs9800806	0.83[EUR][1000 genomes]
rs9800871	0.82[EUR][1000 genomes]
rs9968911	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	esv1803291	chr6:150018508-150164190	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS 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 target site	29 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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:17)

SNP	Gene	Cis/trans	Tissue	Source
rs9371486	GINM1	cis	Whole Blood	GTEx
rs9371486	KATNA1	cis	Muscle Skeletal	GTEx
rs9371486	RAET1G	cis	Thyroid	GTEx
rs9371486	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx
rs9371486	RP11-350J20.5	cis	lung	GTEx
rs9371486	RP11-350J20.9	cis	Esophagus Mucosa	GTEx
rs9371486	C6orf72	Cis_1M	lymphoblastoid	RTeQTL
rs9371486	RP11-350J20.5	cis	Nerve Tibial	GTEx
rs9371486	NUP43	Cis_1M	lymphoblastoid	RTeQTL
rs9371486	RP11-350J20.5	cis	Artery Tibial	GTEx
rs9371486	RP11-350J20.5	cis	Esophagus Mucosa	GTEx
rs9371486	LRP11	cis	Skin Sun Exposed Lower leg	GTEx
rs9371486	RP11-350J20.5	cis	Thyroid	GTEx
rs9371486	NUP43	cis	Whole Blood	GTEx
rs9371486	PCMT1	cis	Esophagus Muscularis	GTEx
rs9371486	RP11-350J20.5	cis	Esophagus Muscularis	GTEx
rs9371486	RP11-350J20.5	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:80 , 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	chr6:150087200-150154000	Weak transcription	Small Intestine	intestine
3	chr6:150088000-150160400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr6:150094400-150167200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr6:150105800-150176400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr6:150112600-150167200	Weak transcription	Colon Smooth Muscle	Colon
7	chr6:150119000-150164000	Weak transcription	Right Ventricle	heart
8	chr6:150120000-150164600	Weak transcription	Fetal Kidney	kidney
9	chr6:150123600-150157000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr6:150123800-150155800	Weak transcription	NH-A	brain
11	chr6:150128000-150157200	Weak transcription	Lung	lung
12	chr6:150132800-150161800	Weak transcription	Fetal Lung	lung
13	chr6:150133000-150157200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr6:150133200-150161200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr6:150133200-150161800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr6:150133200-150162000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr6:150134800-150155400	Weak transcription	Dnd41	blood
18	chr6:150135000-150161600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:150141400-150167200	Weak transcription	Right Atrium	heart
20	chr6:150143200-150157200	Weak transcription	Gastric	stomach
21	chr6:150143600-150161600	Weak transcription	Left Ventricle	heart
22	chr6:150146200-150167000	Weak transcription	Psoas Muscle	Psoas
23	chr6:150147400-150155000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:150147800-150154200	Weak transcription	NHEK	skin
25	chr6:150147800-150155600	Weak transcription	Esophagus	oesophagus
26	chr6:150147800-150156800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr6:150147800-150163600	Weak transcription	Fetal Brain Female	brain
28	chr6:150148000-150155000	Weak transcription	Brain Germinal Matrix	brain
29	chr6:150148200-150155200	Weak transcription	Adipose Nuclei	Adipose
30	chr6:150148800-150154800	Weak transcription	Hela-S3	cervix
31	chr6:150149000-150157200	Weak transcription	Fetal Intestine Large	intestine
32	chr6:150150400-150155000	Weak transcription	Ovary	ovary
33	chr6:150150600-150166400	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr6:150151200-150161600	Weak transcription	Stomach Mucosa	stomach
35	chr6:150151400-150155600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:150151800-150159000	Strong transcription	Placenta	Placenta
37	chr6:150152400-150157000	Weak transcription	Stomach Smooth Muscle	stomach
38	chr6:150152400-150157400	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr6:150152400-150165400	Weak transcription	HSMMtube	muscle
40	chr6:150152600-150153400	Strong transcription	A549	lung
41	chr6:150152600-150156000	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr6:150152600-150158200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr6:150152600-150159000	Strong transcription	Fetal Stomach	stomach
44	chr6:150152600-150161600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr6:150152800-150155000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:150152800-150155000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr6:150152800-150155000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr6:150152800-150155000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr6:150152800-150155200	Weak transcription	Fetal Muscle Leg	muscle
50	chr6:150152800-150155600	Weak transcription	Osteobl	bone

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