Variant report

Variant	rs10054519
Chromosome Location	chr5:43444233-43444234
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:43443335..43445222-chr5:43448398..43451206,3	K562	blood:
2	chr5:43442199..43444663-chr5:43460452..43462412,2	K562	blood:

Extended variants
information (count: 83 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10036954	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10038545	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10053229	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10055801	0.92[JPT][hapmap];1.00[YRI][hapmap]
rs10059912	0.82[EUR][1000 genomes]
rs10059993	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10065689	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10066408	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10068064	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10074682	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10462051	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10472380	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10473310	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10473311	0.90[ASN][1000 genomes]
rs11742171	0.82[JPT][hapmap]
rs11949083	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12187908	0.84[JPT][hapmap]
rs12521249	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.80[EUR][1000 genomes]
rs12697457	0.82[EUR][1000 genomes]
rs13356232	0.85[YRI][hapmap]
rs13359906	0.82[EUR][1000 genomes]
rs1366410	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1389868	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1389869	0.94[ASN][1000 genomes]
rs1389870	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1593971	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2131998	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2132001	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2132003	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28437972	0.91[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs3776423	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3806870	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4072918	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4072919	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs4074777	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4386738	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs4467713	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4535459	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.82[EUR][1000 genomes]
rs4866833	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4866835	0.81[EUR][1000 genomes]
rs55667604	0.82[EUR][1000 genomes]
rs55855322	0.91[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs56008952	0.83[EUR][1000 genomes]
rs56333629	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57403343	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57547662	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs60297702	0.85[EUR][1000 genomes]
rs6451693	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6451695	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6451696	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6451697	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6451698	0.86[JPT][hapmap];0.81[AMR][1000 genomes]
rs6451699	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6451704	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6451705	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66495712	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6858942	0.87[ASN][1000 genomes]
rs6860493	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6862102	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6866325	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs6866802	0.81[EUR][1000 genomes]
rs6869933	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6870018	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6878770	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6884661	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs6885679	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6891363	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6895327	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6896693	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72756535	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73100614	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs750583	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs754301	0.82[CHB][hapmap]
rs7703662	0.82[EUR][1000 genomes]
rs7705166	0.85[CHB][hapmap]
rs7710628	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7713479	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7715782	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7718627	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7732140	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7732656	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7736108	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9885189	0.82[EUR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10054519	NNT	cis	multi-tissue	Pritchard
rs10054519	NNT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 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	chr5:43433200-43454400	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr5:43433200-43460200	Weak transcription	NHLF	lung
4	chr5:43433400-43456000	Weak transcription	Brain Hippocampus Middle	brain
5	chr5:43433600-43452200	Weak transcription	Osteobl	bone
6	chr5:43433800-43483400	Weak transcription	Gastric	stomach
7	chr5:43438400-43451000	Weak transcription	HepG2	liver
8	chr5:43438800-43460600	Weak transcription	NH-A	brain
9	chr5:43440000-43462400	Weak transcription	Colonic Mucosa	Colon
10	chr5:43440800-43466400	Weak transcription	Colon Smooth Muscle	Colon
11	chr5:43440800-43466800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr5:43441600-43466600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr5:43441800-43445000	Weak transcription	HSMM	muscle
14	chr5:43441800-43461000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr5:43442000-43453400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr5:43442000-43460000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr5:43442600-43445000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr5:43442600-43446200	Weak transcription	Fetal Brain Male	brain
19	chr5:43443000-43448400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr5:43443400-43444400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
21	chr5:43443400-43444400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
22	chr5:43443400-43444600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr5:43443400-43444600	ZNF genes & repeats	Fetal Intestine Large	intestine
24	chr5:43443400-43444600	ZNF genes & repeats	Ovary	ovary
25	chr5:43443400-43445200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr5:43443400-43445200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr5:43443400-43446600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
28	chr5:43443400-43446800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr5:43443400-43448000	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr5:43443600-43444400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
31	chr5:43443600-43444400	ZNF genes & repeats	Primary T cells from cord blood	blood
32	chr5:43443600-43444400	Strong transcription	Esophagus	oesophagus
33	chr5:43443600-43444600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
34	chr5:43443600-43444600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr5:43443600-43444600	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
36	chr5:43443600-43444600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr5:43443600-43444600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
38	chr5:43443600-43444600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr5:43443600-43444600	ZNF genes & repeats	Aorta	Aorta
40	chr5:43443600-43444600	ZNF genes & repeats	Fetal Lung	lung
41	chr5:43443600-43444800	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
42	chr5:43443600-43444800	ZNF genes & repeats	Fetal Intestine Small	intestine
43	chr5:43443600-43444800	Strong transcription	Rectal Smooth Muscle	rectum
44	chr5:43443600-43445200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr5:43443600-43445200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
46	chr5:43443600-43446000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
47	chr5:43443600-43448400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr5:43443800-43444400	ZNF genes & repeats	Psoas Muscle	Psoas
49	chr5:43443800-43444600	ZNF genes & repeats	Fetal Stomach	stomach
50	chr5:43443800-43444600	ZNF genes & repeats	Lung	lung

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