Variant report

Variant	rs9717327
Chromosome Location	chr6:149949928-149949929
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:149947741..149950535-chr6:149952808..149954570,2	MCF-7	breast:
2	chr6:149948922..149951262-chr6:149954918..149957641,2	K562	blood:

Extended variants
information (count: 226 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:219)

rs_ID	r²[population]
rs10214845	0.81[EUR][1000 genomes]
rs10747275	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10747276	0.88[EUR][1000 genomes]
rs10782310	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10782311	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10782312	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10782313	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10782314	0.89[EUR][1000 genomes]
rs10782315	0.87[EUR][1000 genomes]
rs10782316	0.88[EUR][1000 genomes]
rs10782317	0.88[EUR][1000 genomes]
rs10782318	0.88[EUR][1000 genomes]
rs1080670	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10872643	0.91[EUR][1000 genomes]
rs10872644	0.89[EUR][1000 genomes]
rs10872645	0.83[EUR][1000 genomes]
rs10872646	0.88[EUR][1000 genomes]
rs10872647	0.86[EUR][1000 genomes]
rs10872648	0.86[EUR][1000 genomes]
rs10872649	0.88[EUR][1000 genomes]
rs10872650	0.88[EUR][1000 genomes]
rs10872651	0.83[EUR][1000 genomes]
rs11155662	0.85[EUR][1000 genomes]
rs11155668	0.93[EUR][1000 genomes]
rs11155669	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11155670	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11155671	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11155674	0.91[EUR][1000 genomes]
rs11155675	0.86[EUR][1000 genomes]
rs11155676	0.84[EUR][1000 genomes]
rs11155677	0.86[EUR][1000 genomes]
rs11155679	0.85[EUR][1000 genomes]
rs11155680	0.82[EUR][1000 genomes]
rs1125	0.89[EUR][1000 genomes]
rs12111376	0.89[EUR][1000 genomes]
rs12174349	0.90[EUR][1000 genomes]
rs12174716	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12175504	0.85[EUR][1000 genomes]
rs12178310	0.87[EUR][1000 genomes]
rs12183664	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12191643	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12193364	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12195866	0.88[EUR][1000 genomes]
rs12200670	0.91[EUR][1000 genomes]
rs12201033	0.92[EUR][1000 genomes]
rs12203703	0.90[EUR][1000 genomes]
rs12205092	0.88[EUR][1000 genomes]
rs12206402	0.94[EUR][1000 genomes]
rs12211511	0.86[EUR][1000 genomes]
rs12234128	0.87[EUR][1000 genomes]
rs12523793	0.83[EUR][1000 genomes]
rs12526675	0.89[EUR][1000 genomes]
rs12528279	0.88[EUR][1000 genomes]
rs12529698	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12660304	0.89[EUR][1000 genomes]
rs12662162	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12662174	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1413654	0.81[EUR][1000 genomes]
rs17745062	0.85[EUR][1000 genomes]
rs1934534	0.91[EUR][1000 genomes]
rs2064520	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2064521	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2065663	0.88[EUR][1000 genomes]
rs2065664	0.81[EUR][1000 genomes]
rs2144207	0.81[EUR][1000 genomes]
rs2185352	0.91[EUR][1000 genomes]
rs2297928	0.90[EUR][1000 genomes]
rs2297930	0.90[EUR][1000 genomes]
rs2297932	0.90[EUR][1000 genomes]
rs34157004	0.91[EUR][1000 genomes]
rs34337297	0.87[EUR][1000 genomes]
rs35031906	0.88[EUR][1000 genomes]
rs35443312	0.88[EUR][1000 genomes]
rs35763894	0.89[EUR][1000 genomes]
rs35830138	0.91[EUR][1000 genomes]
rs35961297	0.91[EUR][1000 genomes]
rs35967444	0.91[EUR][1000 genomes]
rs3734295	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3763161	0.88[EUR][1000 genomes]
rs3777949	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3798761	0.91[EUR][1000 genomes]
rs3805749	0.81[EUR][1000 genomes]
rs3924871	0.91[EUR][1000 genomes]
rs4039600	0.88[EUR][1000 genomes]
rs4354168	0.91[EUR][1000 genomes]
rs4380763	0.91[EUR][1000 genomes]
rs4421206	0.91[EUR][1000 genomes]
rs4455682	0.91[EUR][1000 genomes]
rs4869812	0.91[EUR][1000 genomes]
rs4870139	0.89[EUR][1000 genomes]
rs4870144	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4870267	0.91[EUR][1000 genomes]
rs4870388	0.91[EUR][1000 genomes]
rs4870493	0.91[EUR][1000 genomes]
rs4870509	0.91[EUR][1000 genomes]
rs4870529	0.90[EUR][1000 genomes]
rs55849538	0.93[EUR][1000 genomes]
rs55938765	0.88[EUR][1000 genomes]
rs55993747	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56091542	0.93[EUR][1000 genomes]
rs56397000	0.89[EUR][1000 genomes]
rs57938011	0.93[EUR][1000 genomes]
rs58189451	0.86[EUR][1000 genomes]
rs60424881	0.89[EUR][1000 genomes]
rs62439811	0.94[EUR][1000 genomes]
rs62439836	0.90[EUR][1000 genomes]
rs62439837	0.91[EUR][1000 genomes]
rs62439840	0.91[EUR][1000 genomes]
rs62439842	0.91[EUR][1000 genomes]
rs62439843	0.88[EUR][1000 genomes]
rs62441279	0.90[EUR][1000 genomes]
rs62441284	0.88[EUR][1000 genomes]
rs66516768	0.91[EUR][1000 genomes]
rs6913486	0.91[EUR][1000 genomes]
rs7381555	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7450246	0.91[EUR][1000 genomes]
rs7740278	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7752594	0.90[EUR][1000 genomes]
rs7753812	0.88[EUR][1000 genomes]
rs7754399	0.91[EUR][1000 genomes]
rs7767622	0.91[EUR][1000 genomes]
rs9027	0.86[EUR][1000 genomes]
rs9285521	0.86[EUR][1000 genomes]
rs9285522	0.94[EUR][1000 genomes]
rs9285523	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9285524	0.88[EUR][1000 genomes]
rs9286597	0.81[EUR][1000 genomes]
rs9322189	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9322190	0.80[EUR][1000 genomes]
rs9322192	0.85[EUR][1000 genomes]
rs9322193	0.86[EUR][1000 genomes]
rs9322194	0.85[EUR][1000 genomes]
rs9322196	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9322197	0.90[EUR][1000 genomes]
rs9322198	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9322199	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9322200	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9322204	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9322206	0.90[EUR][1000 genomes]
rs9322207	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9322208	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9322209	0.91[EUR][1000 genomes]
rs9322210	0.91[EUR][1000 genomes]
rs9322214	0.91[EUR][1000 genomes]
rs9322215	0.86[EUR][1000 genomes]
rs9322217	0.81[EUR][1000 genomes]
rs9322220	0.81[EUR][1000 genomes]
rs9322221	0.80[EUR][1000 genomes]
rs9377228	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9377229	0.86[EUR][1000 genomes]
rs9377230	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9379314	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9379348	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9383812	0.91[EUR][1000 genomes]
rs9383844	0.90[EUR][1000 genomes]
rs9393132	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9393175	0.91[EUR][1000 genomes]
rs9399692	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9399693	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9404047	0.89[EUR][1000 genomes]
rs9404048	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9406286	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9406345	0.92[EUR][1000 genomes]
rs9406346	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9478291	0.89[EUR][1000 genomes]
rs9479094	0.88[EUR][1000 genomes]
rs9479494	0.89[EUR][1000 genomes]
rs9479808	0.82[EUR][1000 genomes]
rs9479810	0.85[EUR][1000 genomes]
rs9480009	0.88[EUR][1000 genomes]
rs9480031	0.88[EUR][1000 genomes]
rs9485405	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9485408	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9498382	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9498384	0.89[EUR][1000 genomes]
rs9505823	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9505824	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9505826	0.90[EUR][1000 genomes]
rs9505967	0.91[EUR][1000 genomes]
rs9505972	0.83[EUR][1000 genomes]
rs9505982	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9505983	0.88[EUR][1000 genomes]
rs9688350	0.89[EUR][1000 genomes]
rs9688452	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9688517	0.89[EUR][1000 genomes]
rs9688699	0.89[EUR][1000 genomes]
rs9688750	0.88[EUR][1000 genomes]
rs9688794	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9688858	0.89[EUR][1000 genomes]
rs9688861	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9689084	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9689340	0.89[EUR][1000 genomes]
rs9689599	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9689702	0.89[EUR][1000 genomes]
rs9689716	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9689723	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9718079	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9766004	0.88[EUR][1000 genomes]
rs9766037	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9766525	0.81[EUR][1000 genomes]
rs9766886	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9767105	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9767113	0.90[EUR][1000 genomes]
rs9767122	0.81[EUR][1000 genomes]
rs9767123	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9767309	0.90[EUR][1000 genomes]
rs9767554	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9767555	0.88[EUR][1000 genomes]
rs9767652	0.89[EUR][1000 genomes]
rs9767713	0.89[EUR][1000 genomes]
rs9767727	0.90[EUR][1000 genomes]
rs9800580	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9800603	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9800614	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9800686	0.91[EUR][1000 genomes]
rs9800736	0.91[EUR][1000 genomes]
rs9800806	0.89[EUR][1000 genomes]
rs9800871	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9968911	0.86[AMR][1000 genomes];0.91[EUR][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	nsv289	chr6:149864898-149998818	Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv5534	chr6:149864898-149998818	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	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
4	esv1792620	chr6:149909491-150083621	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	esv3529123	chr6:149946209-149950607	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv3529124	chr6:149946209-149950607	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv3529122	chr6:149946259-149950757	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs9717327	NUP43	Cis_1M	lymphoblastoid	RTeQTL
rs9717327	RP11-350J20.5	cis	Esophagus Mucosa	GTEx
rs9717327	RP11-350J20.5	cis	Artery Aorta	GTEx
rs9717327	RAET1G	cis	Thyroid	GTEx
rs9717327	RP11-350J20.5	cis	Esophagus Muscularis	GTEx
rs9717327	C6orf72	Cis_1M	lymphoblastoid	RTeQTL
rs9717327	RP11-350J20.5	cis	lung	GTEx
rs9717327	RP11-350J20.5	cis	Thyroid	GTEx
rs9717327	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx
rs9717327	RP11-350J20.5	cis	Artery Tibial	GTEx
rs9717327	RP11-350J20.5	cis	Nerve Tibial	GTEx
rs9717327	RP11-350J20.9	cis	Skin Sun Exposed Lower leg	GTEx
rs9717327	NUP43	cis	Whole Blood	GTEx
rs9717327	GINM1	cis	Whole Blood	GTEx
rs9717327	RP11-350J20.5	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149915600-149968400	Weak transcription	Pancreas	Pancrea
2	chr6:149915600-149969200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:149915800-149969200	Weak transcription	Gastric	stomach
4	chr6:149916400-149950200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr6:149918400-149950200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr6:149918800-149967600	Weak transcription	HUVEC	blood vessel
7	chr6:149918800-149967600	Weak transcription	NHLF	lung
8	chr6:149923000-149952200	Weak transcription	NH-A	brain
9	chr6:149924800-149967400	Weak transcription	Colon Smooth Muscle	Colon
10	chr6:149924800-149968000	Weak transcription	Fetal Kidney	kidney
11	chr6:149925200-149967000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr6:149935000-149967000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr6:149935200-149959200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr6:149935200-149966200	Weak transcription	Hela-S3	cervix
15	chr6:149935200-149967800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr6:149935200-149968000	Weak transcription	Brain Angular Gyrus	brain
17	chr6:149935200-149969000	Weak transcription	Small Intestine	intestine
18	chr6:149935400-149958200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:149935400-149968000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr6:149935600-149968000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr6:149935600-149968400	Weak transcription	Esophagus	oesophagus
22	chr6:149935800-149968600	Weak transcription	Aorta	Aorta
23	chr6:149936000-149967000	Weak transcription	Primary hematopoietic stem cells	blood
24	chr6:149936000-149967200	Weak transcription	HMEC	breast
25	chr6:149936000-149968000	Weak transcription	Right Ventricle	heart
26	chr6:149936800-149969000	Weak transcription	Lung	lung
27	chr6:149937400-149968000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr6:149938400-149960800	Weak transcription	Fetal Heart	heart
29	chr6:149940000-149958400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr6:149940200-149954200	Strong transcription	Dnd41	blood
31	chr6:149940400-149950000	Strong transcription	Fetal Stomach	stomach
32	chr6:149941200-149956400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr6:149941400-149953600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr6:149941400-149967600	Weak transcription	Brain Substantia Nigra	brain
35	chr6:149941400-149967600	Weak transcription	Fetal Brain Male	brain
36	chr6:149941400-149968000	Weak transcription	Brain Hippocampus Middle	brain
37	chr6:149942200-149950000	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr6:149942200-149950000	Weak transcription	Fetal Lung	lung
39	chr6:149942200-149967600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr6:149942800-149954000	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr6:149943200-149950000	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr6:149943400-149968000	Weak transcription	Brain Cingulate Gyrus	brain
43	chr6:149943600-149950200	Weak transcription	Fetal Brain Female	brain
44	chr6:149943800-149955400	Weak transcription	Colonic Mucosa	Colon
45	chr6:149944400-149950200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr6:149944600-149950200	Weak transcription	HepG2	liver
47	chr6:149944600-149951000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr6:149944600-149953000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr6:149944600-149953200	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr6:149944600-149953200	Weak transcription	HSMMtube	muscle

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