Variant report

Variant	rs3766096
Chromosome Location	chr1:169341261-169341262
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	chr1:169073561..169077593-chr1:169336088..169341683,7	K562	blood:
2	chr1:169338121..169342264-chr1:169451874..169455112,4	K562	blood:

Variant related genes	Relation type
ENSG00000143153	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10458395	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10458396	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10458397	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489187	0.81[ASN][1000 genomes]
rs10489188	0.81[ASN][1000 genomes]
rs10800439	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10800441	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800446	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919154	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10919155	0.81[ASN][1000 genomes]
rs10919163	0.81[ASN][1000 genomes]
rs10919164	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919167	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1112839	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11799936	0.81[ASN][1000 genomes]
rs11799948	0.81[ASN][1000 genomes]
rs11800843	0.81[ASN][1000 genomes]
rs11808015	0.81[ASN][1000 genomes]
rs12021770	0.81[ASN][1000 genomes]
rs12022776	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12024897	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12026287	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12026728	0.81[ASN][1000 genomes]
rs12027242	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12028813	0.81[ASN][1000 genomes]
rs12030320	0.81[ASN][1000 genomes]
rs12032201	0.81[ASN][1000 genomes]
rs12034986	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12049227	0.81[ASN][1000 genomes]
rs12563090	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12564884	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1517748	0.97[ASN][1000 genomes]
rs16862118	0.81[ASN][1000 genomes]
rs1980198	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2003652	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003654	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2014061	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2275299	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28566091	0.81[ASN][1000 genomes]
rs35269183	0.81[ASN][1000 genomes]
rs3753303	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3818844	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4656670	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61807018	0.81[ASN][1000 genomes]
rs6427186	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427188	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6427189	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6427191	0.81[ASN][1000 genomes]
rs6660945	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6669741	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6677410	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6690801	0.81[ASN][1000 genomes]
rs6696428	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696810	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72702179	0.81[ASN][1000 genomes]
rs72702188	0.81[ASN][1000 genomes]
rs7516248	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7528375	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7528449	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534737	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7535788	0.81[ASN][1000 genomes]
rs7537890	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7539415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554703	0.96[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs961404	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9659035	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv1010010	chr1:169189586-169347545	Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv872531	chr1:169191860-169388193	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv872532	chr1:169275630-169363203	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3766096	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs3766096	NME7	cis	Thyroid	GTEx
rs3766096	BLZF1	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169338000-169351200	Weak transcription	Lung	lung
2	chr1:169338000-169351200	Weak transcription	Spleen	Spleen
3	chr1:169338000-169353600	Weak transcription	Small Intestine	intestine
4	chr1:169338000-169358000	Weak transcription	Esophagus	oesophagus
5	chr1:169338000-169360000	Weak transcription	Fetal Heart	heart
6	chr1:169338000-169360400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:169338000-169365200	Weak transcription	Gastric	stomach
8	chr1:169338000-169365600	Weak transcription	Pancreas	Pancrea
9	chr1:169338200-169341600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:169338200-169345800	Weak transcription	Primary B cells from peripheral blood	blood
11	chr1:169338200-169345800	Weak transcription	Ovary	ovary
12	chr1:169338200-169351800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:169338200-169360400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:169338200-169360400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:169338200-169362200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:169338200-169363600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr1:169338200-169363600	Weak transcription	Stomach Mucosa	stomach
18	chr1:169338200-169369000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr1:169338400-169345800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:169338400-169345800	Weak transcription	Right Ventricle	heart
21	chr1:169338400-169349600	Weak transcription	HSMMtube	muscle
22	chr1:169338400-169360200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr1:169338400-169362600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:169338600-169341600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr1:169338600-169341800	Weak transcription	Fetal Kidney	kidney
26	chr1:169338600-169345800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr1:169338600-169345800	Weak transcription	Colonic Mucosa	Colon
28	chr1:169338600-169345800	Weak transcription	Colon Smooth Muscle	Colon
29	chr1:169338600-169345800	Weak transcription	Psoas Muscle	Psoas
30	chr1:169338600-169346000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr1:169338600-169346000	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr1:169338600-169349800	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr1:169338600-169351400	Weak transcription	Thymus	Thymus
34	chr1:169338600-169352200	Weak transcription	Aorta	Aorta
35	chr1:169338600-169352200	Weak transcription	Fetal Stomach	stomach
36	chr1:169338600-169352400	Weak transcription	Fetal Intestine Small	intestine
37	chr1:169338600-169352800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr1:169338600-169357600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:169338800-169341600	Weak transcription	Primary B cells from cord blood	blood
40	chr1:169338800-169345800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:169338800-169347400	Weak transcription	Fetal Brain Female	brain
42	chr1:169339000-169341400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr1:169339000-169341400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
44	chr1:169339000-169342800	Strong transcription	Liver	Liver
45	chr1:169339000-169342800	Strong transcription	Brain Anterior Caudate	brain
46	chr1:169339000-169342800	Strong transcription	Fetal Lung	lung
47	chr1:169339000-169343000	Strong transcription	Osteobl	bone
48	chr1:169339000-169343400	Strong transcription	Placenta	Placenta
49	chr1:169339000-169344200	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr1:169339200-169341400	Strong transcription	Brain Germinal Matrix	brain

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