Variant report

Variant	rs2050659
Chromosome Location	chr6:79734369-79734370
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:79733598..79735343-chr6:79785922..79787786,2	MCF-7	breast:

Extended variants
information (count: 136 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs1027813	0.84[EUR][1000 genomes]
rs1044309	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10455356	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10755377	0.91[ASN][1000 genomes]
rs10943600	0.88[ASN][1000 genomes]
rs10943605	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10943608	0.91[ASN][1000 genomes]
rs10943609	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10943613	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11752126	0.97[ASN][1000 genomes]
rs11754419	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12153837	0.81[ASN][1000 genomes]
rs12193319	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12196457	0.91[ASN][1000 genomes]
rs12660770	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13191068	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13202531	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13204088	0.93[ASN][1000 genomes]
rs1354831	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1354832	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1413968	0.84[ASN][1000 genomes]
rs1413969	0.84[ASN][1000 genomes]
rs1415859	0.86[ASN][1000 genomes]
rs1538233	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1538235	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1547731	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1567167	0.85[EUR][1000 genomes]
rs1572584	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1572585	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1890229	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1960542	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1984195	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2050660	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2050661	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2050662	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2050663	0.85[AMR][1000 genomes]
rs2063123	0.93[ASN][1000 genomes]
rs2095724	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2105143	0.98[ASN][1000 genomes]
rs2152951	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2174739	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2174742	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2174743	0.91[EUR][1000 genomes]
rs35887627	0.94[ASN][1000 genomes]
rs36128361	0.97[ASN][1000 genomes]
rs3805747	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3902856	0.98[ASN][1000 genomes]
rs4147183	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4415132	0.85[EUR][1000 genomes]
rs4421161	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4565265	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4706079	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4706080	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4706742	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4706743	0.88[ASN][1000 genomes]
rs4706746	0.91[ASN][1000 genomes]
rs4706747	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55755815	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56057971	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6454092	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6912683	0.81[EUR][1000 genomes]
rs6915558	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6926537	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6937465	0.87[EUR][1000 genomes]
rs6940637	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7741943	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7742034	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7742431	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7753358	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7753531	0.84[ASN][1000 genomes]
rs7756858	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7760866	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9341754	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9343843	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9343844	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9343848	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9343856	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9343860	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9343861	0.98[ASN][1000 genomes]
rs9343863	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9343870	0.86[ASN][1000 genomes]
rs9350792	0.82[ASN][1000 genomes]
rs9350794	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9350799	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9350800	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9352664	0.86[EUR][1000 genomes]
rs9352665	0.86[EUR][1000 genomes]
rs9352666	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9352667	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9352669	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9352670	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9352675	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9352676	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9352683	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9352686	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9352691	0.91[ASN][1000 genomes]
rs9352694	0.84[ASN][1000 genomes]
rs9359354	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9359359	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9359360	0.97[ASN][1000 genomes]
rs9359362	0.94[ASN][1000 genomes]
rs9359364	0.86[ASN][1000 genomes]
rs9361451	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9361454	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9361460	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9361462	0.89[EUR][1000 genomes]
rs9361466	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9361467	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9361472	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9361477	0.97[ASN][1000 genomes]
rs9361480	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9361482	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9361488	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9443621	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9443622	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9443626	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9443632	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9443637	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9443638	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9443643	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9443645	0.81[ASN][1000 genomes]
rs9448580	0.84[EUR][1000 genomes]
rs9448584	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9448587	0.91[EUR][1000 genomes]
rs9448588	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9448590	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9448591	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9448596	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9448597	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9448607	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9448610	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs946022	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs971994	0.85[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	nsv1015352	chr6:79521820-79757024	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv830705	chr6:79659297-79829530	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv518477	chr6:79700159-79850427	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2050659	IRAK1BP1	cis	Artery Tibial	GTEx
rs2050659	IRAK1BP1	cis	Artery Aorta	GTEx
rs2050659	IRAK1BP1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:79687000-79736000	Strong transcription	HUES6 Cell Line	embryonic stem cell
2	chr6:79687000-79736200	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr6:79687200-79735400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr6:79687200-79741600	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr6:79687600-79775000	Strong transcription	Dnd41	blood
6	chr6:79687800-79736000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr6:79688400-79742800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr6:79688400-79744400	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr6:79689200-79738800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr6:79704000-79737400	Weak transcription	Right Ventricle	heart
11	chr6:79704600-79786600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:79705000-79738600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr6:79706600-79740000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:79706600-79747800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr6:79707400-79737400	Weak transcription	Spleen	Spleen
16	chr6:79707400-79740000	Weak transcription	Small Intestine	intestine
17	chr6:79707400-79755800	Weak transcription	Pancreas	Pancrea
18	chr6:79707400-79786000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:79707400-79786600	Weak transcription	Esophagus	oesophagus
20	chr6:79707800-79745200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:79708200-79741800	Weak transcription	A549	lung
22	chr6:79708800-79769600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr6:79709000-79737400	Weak transcription	Ovary	ovary
24	chr6:79710800-79774600	Weak transcription	Psoas Muscle	Psoas
25	chr6:79711800-79735000	Weak transcription	Colonic Mucosa	Colon
26	chr6:79712200-79741600	Weak transcription	HSMMtube	muscle
27	chr6:79712400-79735400	Weak transcription	Brain Substantia Nigra	brain
28	chr6:79713600-79747000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr6:79714600-79735800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr6:79714600-79747000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr6:79715800-79735400	Weak transcription	Brain Angular Gyrus	brain
32	chr6:79717200-79765600	Weak transcription	Colon Smooth Muscle	Colon
33	chr6:79718000-79739600	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr6:79721000-79739000	Strong transcription	Primary B cells from peripheral blood	blood
35	chr6:79721600-79735600	Weak transcription	Fetal Heart	heart
36	chr6:79722200-79736000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr6:79722400-79735400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr6:79722400-79735800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr6:79722600-79734400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr6:79722600-79739000	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr6:79723000-79735000	Weak transcription	Brain Hippocampus Middle	brain
42	chr6:79724600-79765200	Weak transcription	Stomach Mucosa	stomach
43	chr6:79725000-79739800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr6:79725200-79747000	Weak transcription	Rectal Smooth Muscle	rectum
45	chr6:79725400-79738200	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr6:79725800-79738600	Weak transcription	NHLF	lung
47	chr6:79726000-79751400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr6:79726000-79765800	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr6:79726400-79737200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr6:79726600-79735600	Weak transcription	Brain Anterior Caudate	brain

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