Variant report

Variant	rs1389868
Chromosome Location	chr5:43458215-43458216
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:43457241..43459237-chr5:43555350..43556899,2	K562	blood:
2	chr5:43458100..43461748-chr5:43479402..43482480,3	MCF-7	breast:
3	chr5:43458177..43460519-chr5:43482121..43483647,2	K562	blood:
4	chr5:43454555..43461346-chr5:43477105..43484022,8	K562	blood:
5	chr5:43449554..43453846-chr5:43454516..43458805,5	K562	blood:
6	chr5:43450668..43452403-chr5:43455966..43458805,2	K562	blood:

Variant related genes	Relation type
ENSG00000172239	Chromatin interaction
ENSG00000151881	Chromatin interaction

Extended variants
information (count: 177 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:176)

rs_ID	r²[population]
rs10036954	0.96[CEU][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10038545	0.90[ASN][1000 genomes]
rs10038608	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10042992	0.96[CEU][hapmap];1.00[YRI][hapmap]
rs10045400	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10045455	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10054519	0.88[ASN][1000 genomes]
rs10055801	0.92[JPT][hapmap]
rs10057103	0.85[CEU][hapmap]
rs10058558	0.96[CEU][hapmap];0.88[YRI][hapmap]
rs10059993	1.00[JPT][hapmap]
rs10061165	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10065689	1.00[JPT][hapmap]
rs10065863	0.85[CEU][hapmap]
rs10068064	1.00[JPT][hapmap]
rs10074682	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10447144	0.96[CEU][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10462051	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.81[EUR][1000 genomes]
rs10472380	0.94[ASN][1000 genomes]
rs10473310	0.94[ASN][1000 genomes]
rs10473311	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10512825	0.84[JPT][hapmap]
rs10512827	0.85[JPT][hapmap]
rs10512828	0.85[JPT][hapmap]
rs1072745	0.86[CEU][hapmap]
rs1072746	0.86[CEU][hapmap]
rs10805672	0.84[JPT][hapmap]
rs10805673	0.84[JPT][hapmap]
rs10805674	0.84[JPT][hapmap]
rs10805675	0.85[JPT][hapmap]
rs10941621	0.84[JPT][hapmap]
rs10941630	0.84[JPT][hapmap]
rs10941631	0.85[JPT][hapmap]
rs10941640	0.96[CEU][hapmap];0.88[YRI][hapmap];0.81[EUR][1000 genomes]
rs11739009	0.84[JPT][hapmap]
rs11741246	0.84[JPT][hapmap]
rs11741797	0.85[JPT][hapmap]
rs11742171	0.91[JPT][hapmap]
rs11742712	0.84[JPT][hapmap]
rs11743633	0.84[JPT][hapmap]
rs11949083	1.00[JPT][hapmap]
rs11950040	0.85[JPT][hapmap]
rs11950448	0.92[JPT][hapmap]
rs11951515	0.83[JPT][hapmap]
rs11956635	0.85[JPT][hapmap]
rs11956988	0.85[JPT][hapmap]
rs12187908	0.84[JPT][hapmap]
rs12332560	0.80[EUR][1000 genomes]
rs12514399	0.83[JPT][hapmap]
rs12515072	0.84[JPT][hapmap]
rs12518032	0.84[JPT][hapmap]
rs12518127	0.85[JPT][hapmap]
rs12521249	1.00[JPT][hapmap]
rs12651879	0.80[EUR][1000 genomes]
rs12652547	0.96[CEU][hapmap]
rs12659369	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12697452	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13185343	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13189004	0.96[CEU][hapmap]
rs13659	0.84[JPT][hapmap]
rs1366410	1.00[JPT][hapmap]
rs1389869	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1389870	0.94[ASN][1000 genomes]
rs1428640	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1545753	0.84[JPT][hapmap]
rs1548097	0.84[JPT][hapmap]
rs1564196	0.84[JPT][hapmap]
rs1564197	0.84[JPT][hapmap]
rs1593971	0.92[JPT][hapmap]
rs17244818	0.84[JPT][hapmap]
rs2013173	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2126948	0.84[JPT][hapmap]
rs2131998	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2131999	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2132000	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2132001	0.82[ASN][1000 genomes]
rs2132003	0.86[ASN][1000 genomes]
rs2172763	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34007811	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35710460	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35881272	0.84[EUR][1000 genomes]
rs36013953	0.86[EUR][1000 genomes]
rs3733769	0.84[JPT][hapmap]
rs3756416	0.85[JPT][hapmap]
rs3776423	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3806870	0.96[CEU][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4072918	1.00[JPT][hapmap]
rs4072919	1.00[JPT][hapmap]
rs4073848	0.96[CEU][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs4073850	0.85[EUR][1000 genomes]
rs4073851	0.80[EUR][1000 genomes]
rs4074777	1.00[JPT][hapmap]
rs4242099	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4288122	0.84[JPT][hapmap]
rs4308491	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4331909	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4367306	0.96[CEU][hapmap]
rs4386738	1.00[JPT][hapmap]
rs4415083	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4467713	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs4535459	1.00[JPT][hapmap]
rs4541663	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4576155	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4866738	0.84[JPT][hapmap]
rs4866746	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4866752	0.85[CEU][hapmap]
rs4866818	0.84[JPT][hapmap]
rs4866820	0.84[JPT][hapmap]
rs4866822	0.92[JPT][hapmap]
rs4866824	0.92[JPT][hapmap]
rs4866833	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs57547662	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57597020	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6451692	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6451693	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6451695	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6451696	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6451697	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6451698	1.00[CEU][hapmap];0.85[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6451699	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6451703	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6451704	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6451705	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6451706	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6451712	0.81[EUR][1000 genomes]
rs6451718	0.85[CEU][hapmap]
rs66495712	0.90[ASN][1000 genomes]
rs67466542	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6814	0.84[JPT][hapmap]
rs6858942	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6859344	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6860493	1.00[JPT][hapmap]
rs6861704	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6862102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6865217	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6866325	1.00[JPT][hapmap]
rs6870018	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6870783	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6878770	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6883661	0.96[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6884661	1.00[JPT][hapmap]
rs6885679	1.00[JPT][hapmap]
rs6886499	0.85[JPT][hapmap]
rs6887351	0.84[JPT][hapmap]
rs6895327	1.00[JPT][hapmap]
rs6896693	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs73100614	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs750582	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs750583	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs750584	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7703662	0.80[AMR][1000 genomes]
rs7707976	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7708369	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7708443	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7708779	0.92[JPT][hapmap]
rs7710628	1.00[JPT][hapmap]
rs7713479	1.00[JPT][hapmap]
rs7714027	0.85[JPT][hapmap]
rs7715782	1.00[JPT][hapmap]
rs7717636	0.80[EUR][1000 genomes]
rs7718627	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7720681	0.85[JPT][hapmap]
rs7724571	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7727047	0.85[JPT][hapmap]
rs7731091	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7732140	0.92[ASN][1000 genomes]
rs7732656	1.00[JPT][hapmap]
rs7734393	0.83[EUR][1000 genomes]
rs7735243	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7736108	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs922439	0.84[JPT][hapmap]
rs9292883	0.86[EUR][1000 genomes]
rs9686159	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9687341	0.80[EUR][1000 genomes]
rs9790987	0.84[JPT][hapmap]
rs9885467	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881017	chr5:43444826-43731692	Weak transcription Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	222 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1389868	NNT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43429400-43460200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:43433200-43460200	Weak transcription	NHLF	lung
3	chr5:43433800-43483400	Weak transcription	Gastric	stomach
4	chr5:43438800-43460600	Weak transcription	NH-A	brain
5	chr5:43440000-43462400	Weak transcription	Colonic Mucosa	Colon
6	chr5:43440800-43466400	Weak transcription	Colon Smooth Muscle	Colon
7	chr5:43440800-43466800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr5:43441600-43466600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr5:43441800-43461000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr5:43442000-43460000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr5:43443800-43459600	Weak transcription	NHDF-Ad	bronchial
12	chr5:43443800-43460200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr5:43443800-43460200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr5:43444000-43459800	Weak transcription	Fetal Thymus	thymus
15	chr5:43444000-43460200	Weak transcription	Duodenum Mucosa	Duodenum
16	chr5:43444000-43460200	Weak transcription	HSMMtube	muscle
17	chr5:43444000-43460200	Weak transcription	K562	blood
18	chr5:43444000-43460200	Weak transcription	NHEK	skin
19	chr5:43444000-43461400	Weak transcription	Spleen	Spleen
20	chr5:43444000-43463600	Weak transcription	Stomach Smooth Muscle	stomach
21	chr5:43444000-43464400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr5:43444000-43467000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr5:43444000-43467000	Weak transcription	Left Ventricle	heart
24	chr5:43444000-43482600	Weak transcription	HMEC	breast
25	chr5:43444200-43460200	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr5:43444200-43467000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr5:43444200-43472600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr5:43444400-43460200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr5:43444400-43463800	Weak transcription	Small Intestine	intestine
30	chr5:43444600-43459200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr5:43444600-43460000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr5:43444600-43460000	Weak transcription	Fetal Lung	lung
33	chr5:43444600-43460200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr5:43444600-43460200	Weak transcription	Pancreas	Pancrea
35	chr5:43444600-43460200	Weak transcription	Thymus	Thymus
36	chr5:43444600-43460600	Weak transcription	Fetal Stomach	stomach
37	chr5:43444600-43460800	Weak transcription	Lung	lung
38	chr5:43444600-43463600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr5:43444600-43466800	Weak transcription	Brain Angular Gyrus	brain
40	chr5:43444800-43466600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr5:43444800-43482600	Weak transcription	Rectal Smooth Muscle	rectum
42	chr5:43445200-43460200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr5:43445200-43466800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr5:43446600-43460000	Weak transcription	Ovary	ovary
45	chr5:43446600-43461800	Weak transcription	Right Ventricle	heart
46	chr5:43446800-43459200	Weak transcription	Dnd41	blood
47	chr5:43446800-43460200	Weak transcription	Hela-S3	cervix
48	chr5:43448200-43459200	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr5:43448200-43467400	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr5:43448200-43471800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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