Variant report

Variant	rs4039600
Chromosome Location	chr6:149897455-149897456
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	chr6:149887638..149889418-chr6:149897443..149899421,2	MCF-7	breast:

Extended variants
information (count: 277 )
Associated
traits (count: 14 )

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

rs_ID	r²[population]
rs10214845	0.83[EUR][1000 genomes]
rs10452626	0.87[EUR][1000 genomes]
rs10457850	0.87[EUR][1000 genomes]
rs10457851	0.87[EUR][1000 genomes]
rs10747275	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10747276	0.89[EUR][1000 genomes]
rs10782310	0.90[EUR][1000 genomes]
rs10782311	0.92[EUR][1000 genomes]
rs10782312	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10782313	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10782314	0.90[EUR][1000 genomes]
rs10782315	0.88[EUR][1000 genomes]
rs10782316	0.89[EUR][1000 genomes]
rs10782317	0.89[EUR][1000 genomes]
rs10782318	0.89[EUR][1000 genomes]
rs1080670	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10872643	0.92[EUR][1000 genomes]
rs10872644	0.90[EUR][1000 genomes]
rs10872645	0.90[EUR][1000 genomes]
rs10872646	0.89[EUR][1000 genomes]
rs10872647	0.88[EUR][1000 genomes]
rs10872648	0.88[EUR][1000 genomes]
rs10872649	0.89[EUR][1000 genomes]
rs10872650	0.89[EUR][1000 genomes]
rs10872651	0.83[EUR][1000 genomes]
rs10872652	0.87[EUR][1000 genomes]
rs10872653	0.84[EUR][1000 genomes]
rs1112729	0.87[EUR][1000 genomes]
rs1112730	0.87[EUR][1000 genomes]
rs11155662	0.85[EUR][1000 genomes]
rs11155668	0.92[EUR][1000 genomes]
rs11155669	0.93[EUR][1000 genomes]
rs11155670	0.92[EUR][1000 genomes]
rs11155671	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11155674	0.92[EUR][1000 genomes]
rs11155675	0.88[EUR][1000 genomes]
rs11155676	0.83[EUR][1000 genomes]
rs11155677	0.87[EUR][1000 genomes]
rs11155679	0.87[EUR][1000 genomes]
rs11155680	0.85[EUR][1000 genomes]
rs11155681	0.81[EUR][1000 genomes]
rs11155682	0.82[EUR][1000 genomes]
rs11155683	0.85[EUR][1000 genomes]
rs11155685	0.86[EUR][1000 genomes]
rs1125	0.91[EUR][1000 genomes]
rs12111376	0.90[EUR][1000 genomes]
rs12174349	0.91[EUR][1000 genomes]
rs12174716	0.94[EUR][1000 genomes]
rs12175504	0.93[EUR][1000 genomes]
rs12175575	0.86[EUR][1000 genomes]
rs12178310	0.88[EUR][1000 genomes]
rs12179031	0.85[EUR][1000 genomes]
rs12182220	0.81[EUR][1000 genomes]
rs12183664	0.92[EUR][1000 genomes]
rs12191643	0.93[EUR][1000 genomes]
rs12193364	0.88[EUR][1000 genomes]
rs12195866	0.95[EUR][1000 genomes]
rs12200670	0.92[EUR][1000 genomes]
rs12201033	0.91[EUR][1000 genomes]
rs12203703	0.91[EUR][1000 genomes]
rs12205092	0.89[EUR][1000 genomes]
rs12206402	0.93[EUR][1000 genomes]
rs12211511	0.93[EUR][1000 genomes]
rs12213779	0.87[EUR][1000 genomes]
rs12234128	0.86[EUR][1000 genomes]
rs12523793	0.83[EUR][1000 genomes]
rs12525871	0.87[EUR][1000 genomes]
rs12526675	0.90[EUR][1000 genomes]
rs12528279	0.89[EUR][1000 genomes]
rs12529698	0.94[EUR][1000 genomes]
rs12660304	0.90[EUR][1000 genomes]
rs12662162	0.90[EUR][1000 genomes]
rs12662174	0.93[EUR][1000 genomes]
rs13215691	0.81[EUR][1000 genomes]
rs1413654	0.83[EUR][1000 genomes]
rs17672976	0.87[EUR][1000 genomes]
rs17745062	0.86[EUR][1000 genomes]
rs1934534	0.92[EUR][1000 genomes]
rs2064520	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2064521	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2065663	0.89[EUR][1000 genomes]
rs2065664	0.87[EUR][1000 genomes]
rs2144207	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2184369	0.86[EUR][1000 genomes]
rs2185352	0.92[EUR][1000 genomes]
rs2297928	0.91[EUR][1000 genomes]
rs2297930	0.91[EUR][1000 genomes]
rs2297932	0.91[EUR][1000 genomes]
rs2342860	0.86[EUR][1000 genomes]
rs2342861	0.86[EUR][1000 genomes]
rs34157004	0.92[EUR][1000 genomes]
rs34337297	0.92[EUR][1000 genomes]
rs35031906	0.95[EUR][1000 genomes]
rs35443312	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35763894	0.89[EUR][1000 genomes]
rs35830138	0.92[EUR][1000 genomes]
rs35961297	0.92[EUR][1000 genomes]
rs35967444	0.92[EUR][1000 genomes]
rs3734295	0.85[EUR][1000 genomes]
rs3763161	0.88[EUR][1000 genomes]
rs3777949	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3798761	0.92[EUR][1000 genomes]
rs3805748	0.86[EUR][1000 genomes]
rs3805749	0.82[EUR][1000 genomes]
rs3805750	0.81[EUR][1000 genomes]
rs3805751	0.81[EUR][1000 genomes]
rs3828700	0.81[EUR][1000 genomes]
rs3924871	0.92[EUR][1000 genomes]
rs4354168	0.92[EUR][1000 genomes]
rs4380763	0.92[EUR][1000 genomes]
rs4421206	0.92[EUR][1000 genomes]
rs4455682	0.92[EUR][1000 genomes]
rs4642491	0.86[EUR][1000 genomes]
rs4816	0.81[EUR][1000 genomes]
rs4869812	0.92[EUR][1000 genomes]
rs4869923	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4869966	0.87[EUR][1000 genomes]
rs4870139	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4870144	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4870267	0.92[EUR][1000 genomes]
rs4870388	0.92[EUR][1000 genomes]
rs4870493	0.92[EUR][1000 genomes]
rs4870509	0.92[EUR][1000 genomes]
rs4870529	0.91[EUR][1000 genomes]
rs55763431	0.86[EUR][1000 genomes]
rs55849538	0.93[EUR][1000 genomes]
rs55938765	0.89[EUR][1000 genomes]
rs55993747	0.92[EUR][1000 genomes]
rs56091542	0.93[EUR][1000 genomes]
rs56374774	0.86[EUR][1000 genomes]
rs56397000	0.90[EUR][1000 genomes]
rs57938011	0.93[EUR][1000 genomes]
rs58189451	0.92[EUR][1000 genomes]
rs60424881	0.90[EUR][1000 genomes]
rs62439811	0.93[EUR][1000 genomes]
rs62439836	0.90[EUR][1000 genomes]
rs62439837	0.92[EUR][1000 genomes]
rs62439840	0.92[EUR][1000 genomes]
rs62439842	0.92[EUR][1000 genomes]
rs62439843	0.95[EUR][1000 genomes]
rs62441279	0.91[EUR][1000 genomes]
rs62441284	0.89[EUR][1000 genomes]
rs62441303	0.87[EUR][1000 genomes]
rs62441335	0.81[EUR][1000 genomes]
rs66516768	0.92[EUR][1000 genomes]
rs6913486	0.92[EUR][1000 genomes]
rs7381555	0.85[EUR][1000 genomes]
rs7450246	0.92[EUR][1000 genomes]
rs7740278	0.93[EUR][1000 genomes]
rs7744015	0.86[EUR][1000 genomes]
rs7752594	0.90[EUR][1000 genomes]
rs7753812	0.95[EUR][1000 genomes]
rs7754399	0.92[EUR][1000 genomes]
rs7767622	0.92[EUR][1000 genomes]
rs9027	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9285521	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9285522	0.93[EUR][1000 genomes]
rs9285523	0.90[EUR][1000 genomes]
rs9285524	0.95[EUR][1000 genomes]
rs9286597	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9322189	0.88[EUR][1000 genomes]
rs9322190	0.81[EUR][1000 genomes]
rs9322192	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9322193	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9322194	0.85[EUR][1000 genomes]
rs9322196	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9322197	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9322198	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9322199	0.80[EUR][1000 genomes]
rs9322200	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9322204	0.93[EUR][1000 genomes]
rs9322206	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9322207	0.92[EUR][1000 genomes]
rs9322208	0.92[EUR][1000 genomes]
rs9322209	0.92[EUR][1000 genomes]
rs9322210	0.92[EUR][1000 genomes]
rs9322214	0.92[EUR][1000 genomes]
rs9322215	0.93[EUR][1000 genomes]
rs9322217	0.81[EUR][1000 genomes]
rs9322218	0.85[EUR][1000 genomes]
rs9322219	0.86[EUR][1000 genomes]
rs9322220	0.83[EUR][1000 genomes]
rs9322221	0.83[EUR][1000 genomes]
rs9372044	0.86[EUR][1000 genomes]
rs9377228	0.89[EUR][1000 genomes]
rs9377229	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9377230	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9379314	0.87[EUR][1000 genomes]
rs9379348	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9383812	0.92[EUR][1000 genomes]
rs9383844	0.91[EUR][1000 genomes]
rs9393132	0.92[EUR][1000 genomes]
rs9393175	0.92[EUR][1000 genomes]
rs9399692	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9399693	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9404047	0.89[EUR][1000 genomes]
rs9404048	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9406286	0.93[EUR][1000 genomes]
rs9406345	0.92[EUR][1000 genomes]
rs9406346	0.92[EUR][1000 genomes]
rs9478291	0.89[EUR][1000 genomes]
rs9479094	0.89[EUR][1000 genomes]
rs9479494	0.90[EUR][1000 genomes]
rs9479808	0.81[EUR][1000 genomes]
rs9479810	0.92[EUR][1000 genomes]
rs9480009	0.89[EUR][1000 genomes]
rs9480031	0.89[EUR][1000 genomes]
rs9485405	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9485408	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9498382	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9498384	0.89[EUR][1000 genomes]
rs9505823	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9505824	0.93[EUR][1000 genomes]
rs9505826	0.89[EUR][1000 genomes]
rs9505967	0.92[EUR][1000 genomes]
rs9505972	0.83[EUR][1000 genomes]
rs9505974	0.84[EUR][1000 genomes]
rs9505975	0.82[EUR][1000 genomes]
rs9505982	0.92[EUR][1000 genomes]
rs9505983	0.95[EUR][1000 genomes]
rs9688350	0.90[EUR][1000 genomes]
rs9688452	0.92[EUR][1000 genomes]
rs9688517	0.90[EUR][1000 genomes]
rs9688699	0.90[EUR][1000 genomes]
rs9688750	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9688794	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9688809	0.80[EUR][1000 genomes]
rs9688858	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9688861	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9688867	0.86[EUR][1000 genomes]
rs9688938	0.80[EUR][1000 genomes]
rs9688940	0.80[EUR][1000 genomes]
rs9689025	0.81[EUR][1000 genomes]
rs9689036	0.85[EUR][1000 genomes]
rs9689084	0.93[EUR][1000 genomes]
rs9689242	0.80[EUR][1000 genomes]
rs9689269	0.81[EUR][1000 genomes]
rs9689340	0.90[EUR][1000 genomes]
rs9689447	0.82[EUR][1000 genomes]
rs9689599	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9689694	0.84[EUR][1000 genomes]
rs9689702	0.90[EUR][1000 genomes]
rs9689716	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9689723	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9717327	0.88[EUR][1000 genomes]
rs9718079	0.88[EUR][1000 genomes]
rs9765861	0.82[EUR][1000 genomes]
rs9765929	0.87[EUR][1000 genomes]
rs9765965	0.86[EUR][1000 genomes]
rs9766004	0.89[EUR][1000 genomes]
rs9766037	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9766214	0.86[EUR][1000 genomes]
rs9766444	0.86[EUR][1000 genomes]
rs9766525	0.83[EUR][1000 genomes]
rs9766886	0.93[EUR][1000 genomes]
rs9767105	0.91[EUR][1000 genomes]
rs9767113	0.91[EUR][1000 genomes]
rs9767122	0.83[EUR][1000 genomes]
rs9767123	0.92[EUR][1000 genomes]
rs9767192	0.80[EUR][1000 genomes]
rs9767309	0.91[EUR][1000 genomes]
rs9767554	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9767555	0.88[EUR][1000 genomes]
rs9767652	0.90[EUR][1000 genomes]
rs9767713	0.89[EUR][1000 genomes]
rs9767727	0.91[EUR][1000 genomes]
rs9800580	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9800603	0.93[EUR][1000 genomes]
rs9800614	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9800686	0.91[EUR][1000 genomes]
rs9800736	0.92[EUR][1000 genomes]
rs9800806	0.90[EUR][1000 genomes]
rs9800871	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9968911	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs4039600	GINM1	cis	Whole Blood	GTEx
rs4039600	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx
rs4039600	RP11-350J20.5	cis	Artery Aorta	GTEx
rs4039600	NUP43	cis	Whole Blood	GTEx
rs4039600	RP11-350J20.5	cis	Esophagus Mucosa	GTEx
rs4039600	RP11-350J20.5	cis	lung	GTEx
rs4039600	NUP43	Cis_1M	lymphoblastoid	RTeQTL
rs4039600	RP11-350J20.5	cis	Esophagus Muscularis	GTEx
rs4039600	C6orf72	Cis_1M	lymphoblastoid	RTeQTL
rs4039600	RP11-350J20.5	cis	Nerve Tibial	GTEx
rs4039600	RP11-350J20.5	cis	Stomach	GTEx
rs4039600	RP11-350J20.5	cis	Adipose Subcutaneous	GTEx
rs4039600	RP11-350J20.5	cis	Artery Tibial	GTEx
rs4039600	RP11-350J20.5	cis	Thyroid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149888400-149901600	Weak transcription	Aorta	Aorta
2	chr6:149888400-149902000	Weak transcription	Gastric	stomach
3	chr6:149888400-149911600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:149888600-149898000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr6:149888600-149898400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:149888600-149901400	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr6:149888600-149901400	Weak transcription	Colonic Mucosa	Colon
8	chr6:149888600-149901600	Weak transcription	NH-A	brain
9	chr6:149888600-149905200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr6:149888600-149907600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:149888600-149909800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr6:149888600-149912800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr6:149888600-149922000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr6:149888800-149898000	Weak transcription	Fetal Kidney	kidney
15	chr6:149888800-149898200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr6:149888800-149898200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr6:149888800-149898200	Weak transcription	Esophagus	oesophagus
18	chr6:149888800-149901400	Weak transcription	Fetal Brain Female	brain
19	chr6:149888800-149901600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr6:149888800-149901600	Weak transcription	NHLF	lung
21	chr6:149888800-149901800	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr6:149888800-149904800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr6:149888800-149914800	Weak transcription	A549	lung
24	chr6:149889000-149897600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr6:149889000-149898200	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr6:149889000-149898400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr6:149889000-149901400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr6:149889000-149901600	Weak transcription	NHDF-Ad	bronchial
29	chr6:149889000-149902000	Weak transcription	Osteobl	bone
30	chr6:149889000-149905400	Weak transcription	HSMMtube	muscle
31	chr6:149889000-149908400	Weak transcription	Pancreas	Pancrea
32	chr6:149889000-149928000	Weak transcription	Stomach Mucosa	stomach
33	chr6:149889200-149897600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:149889200-149898000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr6:149889200-149898400	Weak transcription	Fetal Lung	lung
36	chr6:149889200-149919600	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr6:149889400-149897800	Weak transcription	Brain Germinal Matrix	brain
38	chr6:149889400-149898000	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr6:149889400-149898000	Weak transcription	HSMM	muscle
40	chr6:149889400-149898200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr6:149889400-149901200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr6:149889400-149901600	Weak transcription	Colon Smooth Muscle	Colon
43	chr6:149889400-149911800	Weak transcription	Psoas Muscle	Psoas
44	chr6:149889400-149924200	Weak transcription	Fetal Heart	heart
45	chr6:149889600-149914200	Weak transcription	Hela-S3	cervix
46	chr6:149889600-149931400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr6:149891200-149911200	Weak transcription	Small Intestine	intestine
48	chr6:149891600-149898200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:149892200-149901400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr6:149893200-149899200	Strong transcription	Primary B cells from peripheral blood	blood

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