Variant report

Variant	rs7378662
Chromosome Location	chr5:70810048-70810049
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10044572	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10055460	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10060578	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10064099	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10077085	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10434642	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10474383	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10805884	0.95[EUR][1000 genomes]
rs10942284	0.88[EUR][1000 genomes]
rs10942533	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10942682	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10942700	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10942702	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10942705	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11743135	0.93[EUR][1000 genomes]
rs11746722	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12152748	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12514732	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12516456	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12652715	0.85[ASN][1000 genomes]
rs13157835	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3748043	0.93[EUR][1000 genomes]
rs4062889	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4505929	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5005863	0.86[EUR][1000 genomes]
rs62361818	0.83[ASN][1000 genomes]
rs6452722	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6452900	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6453013	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6453014	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6453018	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6453035	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6871148	0.84[ASN][1000 genomes]
rs6872235	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6872671	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6877289	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6877773	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6886336	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6898471	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs715747	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7380115	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7380280	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7444322	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7447726	0.88[EUR][1000 genomes]
rs7448422	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7449316	0.85[ASN][1000 genomes]
rs7714527	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7715648	0.88[EUR][1000 genomes]
rs7721179	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7727576	0.88[EUR][1000 genomes]
rs7728577	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7735544	0.86[EUR][1000 genomes]
rs9968768	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034703	chr5:70391173-70995695	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv882176	chr5:70738250-70860665	Genic enhancers Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2754424	chr5:70749744-70885544	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv830340	chr5:70797113-70967110	Weak transcription Strong transcription Flanking Active TSS 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 miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv882177	chr5:70800538-70856378	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv882178	chr5:70806958-70856378	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
7	nsv882179	chr5:70807073-70856378	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7378662	MCCC2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:70754200-70815800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:70754400-70824200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr5:70754600-70820400	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr5:70754600-70820400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr5:70759800-70833400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr5:70765400-70820400	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr5:70765400-70820400	Strong transcription	Primary B cells from peripheral blood	blood
8	chr5:70766000-70820400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr5:70771400-70820400	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr5:70774400-70820400	Strong transcription	Fetal Thymus	thymus
11	chr5:70775600-70821000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr5:70776400-70819200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr5:70776400-70820400	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr5:70776400-70820400	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr5:70776400-70820400	Strong transcription	Duodenum Mucosa	Duodenum
16	chr5:70776600-70820400	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr5:70776800-70820400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr5:70776800-70820400	Strong transcription	Dnd41	blood
19	chr5:70777600-70837600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr5:70777800-70816400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr5:70778400-70816400	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr5:70778400-70869600	Weak transcription	Stomach Mucosa	stomach
23	chr5:70779000-70820400	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr5:70779000-70820600	Strong transcription	Liver	Liver
25	chr5:70779200-70812400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr5:70779200-70820600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr5:70779400-70820400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr5:70780000-70820400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr5:70780200-70820400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr5:70783000-70811200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr5:70788000-70819000	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr5:70789600-70825400	Weak transcription	Fetal Heart	heart
33	chr5:70790200-70816800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr5:70790400-70820400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr5:70790600-70812800	Strong transcription	Fetal Lung	lung
36	chr5:70790800-70820400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr5:70795000-70812400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr5:70795000-70820400	Strong transcription	Osteobl	bone
39	chr5:70796200-70825400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr5:70796400-70820400	Strong transcription	Adipose Nuclei	Adipose
41	chr5:70796600-70820400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr5:70796800-70819800	Weak transcription	Pancreas	Pancrea
43	chr5:70796800-70820400	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr5:70796800-70820400	Strong transcription	Placenta	Placenta
45	chr5:70797600-70820400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr5:70798000-70815800	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr5:70798200-70812600	Strong transcription	HSMM	muscle
48	chr5:70799400-70840000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr5:70799600-70820400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr5:70799800-70819000	Weak transcription	H9 Cell Line	embryonic stem cell

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