Variant report

Variant	rs12652715
Chromosome Location	chr5:70896391-70896392
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:70880133..70886735-chr5:70895650..70901637,10	MCF-7	breast:
2	chr5:70881577..70886916-chr5:70891929..70900227,16	MCF-7	breast:
3	chr5:70895778..70897712-chr9:33164777..33166859,2	MCF-7	breast:
4	chr5:70889920..70891594-chr5:70895100..70896727,2	K562	blood:
5	chr5:70883126..70884922-chr5:70895512..70898133,2	K562	blood:

Variant related genes	Relation type
ENSG00000131844	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10055460	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10064099	0.81[ASN][1000 genomes]
rs10071645	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10073617	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10077085	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10434642	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10474383	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10805884	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs10942682	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10942700	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10942702	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs10942705	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs11746722	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12152748	0.87[AFR][1000 genomes]
rs12153571	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13157835	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs1553314	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2270920	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4062889	0.86[AMR][1000 genomes]
rs4505929	0.86[AMR][1000 genomes]
rs62361818	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6452900	0.81[AMR][1000 genomes]
rs6453018	0.85[ASN][1000 genomes]
rs6453035	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs6453043	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6872235	0.85[ASN][1000 genomes]
rs6872671	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6877773	0.85[ASN][1000 genomes]
rs6886336	0.85[ASN][1000 genomes]
rs6898471	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs715747	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7378662	0.85[ASN][1000 genomes]
rs7380115	0.85[ASN][1000 genomes]
rs7380280	0.85[ASN][1000 genomes]
rs7444180	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7444322	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7446049	0.88[EUR][1000 genomes]
rs7448422	0.86[AMR][1000 genomes]
rs7449295	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7449316	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7714527	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9968768	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12652715	MCCC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:70883800-70896400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr5:70883800-70906600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:70883800-70916400	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr5:70884000-70900000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:70884600-70906600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr5:70884800-70896400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr5:70884800-70896400	Weak transcription	Stomach Mucosa	stomach
8	chr5:70884800-70934800	Weak transcription	Fetal Brain Male	brain
9	chr5:70885200-70896400	Weak transcription	Fetal Heart	heart
10	chr5:70885200-70899600	Weak transcription	Brain Substantia Nigra	brain
11	chr5:70885400-70896600	Weak transcription	Psoas Muscle	Psoas
12	chr5:70885400-70896600	Weak transcription	K562	blood
13	chr5:70885400-70899800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr5:70885800-70896600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr5:70886200-70896600	Weak transcription	Small Intestine	intestine
16	chr5:70887000-70896400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr5:70888600-70900400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr5:70888600-70901000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr5:70888800-70896400	Strong transcription	Liver	Liver
20	chr5:70889000-70897000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr5:70889600-70896400	Strong transcription	Dnd41	blood
22	chr5:70889600-70896600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr5:70889800-70900000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr5:70890400-70900400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr5:70891400-70897200	Strong transcription	Fetal Thymus	thymus
26	chr5:70891400-70900000	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr5:70891400-70900400	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr5:70891400-70900400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr5:70892000-70896600	Strong transcription	Adipose Nuclei	Adipose
30	chr5:70892000-70896600	Strong transcription	Left Ventricle	heart
31	chr5:70892000-70896600	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr5:70892000-70896600	Strong transcription	Skeletal Muscle Male	skeletal muscle
33	chr5:70892000-70896800	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr5:70892000-70897000	Strong transcription	Placenta	Placenta
35	chr5:70892000-70900200	Strong transcription	Fetal Muscle Trunk	muscle
36	chr5:70892000-70900400	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr5:70892000-70900400	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr5:70892000-70900400	Strong transcription	Primary B cells from peripheral blood	blood
39	chr5:70892000-70900400	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr5:70892000-70900400	Strong transcription	Stomach Smooth Muscle	stomach
41	chr5:70892000-70900400	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr5:70892200-70896400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr5:70892200-70896600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr5:70892200-70896600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr5:70892200-70897600	Strong transcription	Lung	lung
46	chr5:70892200-70899400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr5:70892200-70900200	Strong transcription	Fetal Intestine Large	intestine
48	chr5:70892200-70900400	Strong transcription	Primary T cells from cord blood	blood
49	chr5:70892200-70900400	Strong transcription	Brain Anterior Caudate	brain
50	chr5:70892200-70900400	Strong transcription	Duodenum Mucosa	Duodenum

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