Variant report

Variant	rs10066408
Chromosome Location	chr5:43495684-43495685
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HEY1	chr5:43495152-43496644	K562	blood:	n/a	n/a
2	ZBTB33	chr5:43494898-43496735	K562	blood:	n/a	n/a
3	POLR2A	chr5:43495536-43495698	A549	lung:	n/a	n/a
4	IRF4	chr5:43495432-43495896	GM12878	blood:	n/a	n/a
5	POLR2A	chr5:43494914-43496199	GM12878	blood:	n/a	n/a
6	HEY1	chr5:43495468-43495802	HepG2	liver:	n/a	n/a
7	POLR2A	chr5:43495103-43496065	GM12891	blood:	n/a	n/a
8	POLR2A	chr5:43495119-43496589	H1-hESC	embryonic stem cell:	n/a	n/a
9	GABPA	chr5:43495373-43495691	Hela-S3	cervix:	n/a	n/a
10	HEY1	chr5:43495432-43495862	K562	blood:	n/a	n/a
11	POLR2A	chr5:43494763-43496825	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr5:43495495-43495824	HepG2	liver:	n/a	n/a
13	POLR2A	chr5:43494936-43496658	GM12892	blood:	n/a	n/a
14	POU2F2	chr5:43495349-43495895	GM12878	blood:	n/a	n/a
15	POU2F2	chr5:43495535-43495705	GM12878	blood:	n/a	n/a
16	POLR2A	chr5:43495490-43495880	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr5:43495389-43495954	GM12891	blood:	n/a	n/a
18	GATA2	chr5:43495468-43495817	K562	blood:	n/a	n/a
19	POLR2A	chr5:43495174-43496206	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr5:43495040-43496668	GM12878	blood:	n/a	n/a
21	POLR2A	chr5:43495036-43496635	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr5:43495158-43496627	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr5:43495233-43496683	GM12892	blood:	n/a	n/a
24	POLR2A	chr5:43495517-43496008	GM12878	blood:	n/a	n/a
25	POLR2A	chr5:43495505-43495956	GM12878	blood:	n/a	n/a
26	POLR2A	chr5:43495418-43496629	GM12891	blood:	n/a	n/a
27	POLR2A	chr5:43495094-43496668	GM12892	blood:	n/a	n/a

Variant related genes	Relation type
C5orf34	TF binding region

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10036954	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10038545	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10053229	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10054519	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10059912	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10068064	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10074682	0.81[ASN][1000 genomes]
rs10462051	0.88[ASN][1000 genomes]
rs10472380	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10473310	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10473311	0.88[ASN][1000 genomes]
rs12332560	0.88[ASN][1000 genomes]
rs12521249	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12651879	0.90[ASN][1000 genomes]
rs12697457	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13189484	0.81[EUR][1000 genomes]
rs13359906	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1389869	0.84[ASN][1000 genomes]
rs1389870	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1593971	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2131998	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2132000	0.82[ASN][1000 genomes]
rs2132001	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2132003	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28437972	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3776423	1.00[ASN][1000 genomes]
rs4072918	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4072919	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4074777	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4331909	0.92[ASN][1000 genomes]
rs4386738	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4428418	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4467713	0.92[ASN][1000 genomes]
rs4535459	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4866830	0.82[ASN][1000 genomes]
rs4866831	0.86[ASN][1000 genomes]
rs4866833	0.92[ASN][1000 genomes]
rs4866835	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55667604	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55855322	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56008952	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56097465	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56333629	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57403343	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57547662	0.84[ASN][1000 genomes]
rs59001943	0.92[ASN][1000 genomes]
rs59224335	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60297702	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6451695	0.84[ASN][1000 genomes]
rs6451696	0.84[ASN][1000 genomes]
rs6451697	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6451699	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6451704	0.92[ASN][1000 genomes]
rs6451705	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6451712	0.92[ASN][1000 genomes]
rs66495712	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67466542	1.00[ASN][1000 genomes]
rs67581152	0.86[ASN][1000 genomes]
rs6858942	0.88[ASN][1000 genomes]
rs6862102	0.83[ASN][1000 genomes]
rs6866325	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6866802	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6869933	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6870018	0.84[ASN][1000 genomes]
rs6878770	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6884661	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6885679	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6891363	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6895327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6896693	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72756535	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs750583	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7710628	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7713479	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7715782	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7717636	0.88[ASN][1000 genomes]
rs7718627	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7732140	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7736108	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7736615	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7737793	0.83[EUR][1000 genomes]
rs9687341	0.87[ASN][1000 genomes]
rs9885189	0.87[EUR][1000 genomes];0.88[ASN][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	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
2	nsv830275	chr5:43469511-43639384	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	220 gene(s)	inside rSNPs	diseases
3	nsv964848	chr5:43495039-43497079	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10066408	NNT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43484800-43498000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:43484800-43502800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr5:43484800-43502800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr5:43484800-43502800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr5:43484800-43502800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr5:43484800-43505600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr5:43484800-43511000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:43484800-43514000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr5:43484800-43514600	Weak transcription	Ovary	ovary
10	chr5:43484800-43514800	Weak transcription	Spleen	Spleen
11	chr5:43485000-43497800	Weak transcription	Placenta	Placenta
12	chr5:43485000-43501000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr5:43485000-43501000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr5:43485000-43502600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr5:43485000-43503000	Weak transcription	NHEK	skin
16	chr5:43485000-43503400	Weak transcription	Brain Germinal Matrix	brain
17	chr5:43485000-43504600	Weak transcription	Fetal Muscle Leg	muscle
18	chr5:43485000-43505000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr5:43485000-43513400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr5:43485000-43513800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr5:43485000-43514200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr5:43485200-43502800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr5:43485200-43505400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr5:43485200-43505400	Weak transcription	Fetal Intestine Large	intestine
25	chr5:43485200-43505400	Weak transcription	Fetal Stomach	stomach
26	chr5:43485200-43506000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr5:43485200-43506000	Weak transcription	Adipose Nuclei	Adipose
28	chr5:43485200-43513200	Weak transcription	NHDF-Ad	bronchial
29	chr5:43485200-43513200	Weak transcription	NHLF	lung
30	chr5:43485200-43513400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr5:43485200-43513400	Weak transcription	Fetal Lung	lung
32	chr5:43485200-43513600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr5:43485200-43513600	Weak transcription	Fetal Intestine Small	intestine
34	chr5:43485200-43513600	Weak transcription	HSMM	muscle
35	chr5:43485200-43513600	Weak transcription	NH-A	brain
36	chr5:43485200-43514200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr5:43485400-43495800	Weak transcription	Colon Smooth Muscle	Colon
38	chr5:43485400-43501200	Weak transcription	A549	lung
39	chr5:43485400-43502800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr5:43485400-43505400	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr5:43485400-43514200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr5:43485800-43503000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr5:43485800-43505200	Weak transcription	Primary B cells from peripheral blood	blood
44	chr5:43485800-43505600	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr5:43485800-43514200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr5:43486000-43497600	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr5:43486000-43501200	Weak transcription	Osteobl	bone
48	chr5:43486000-43503000	Weak transcription	Thymus	Thymus
49	chr5:43486000-43509800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr5:43486000-43514200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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