Variant report

Variant	rs12153571
Chromosome Location	chr5:70885973-70885974
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr5:70885945-70885978	NB4	blood:	n/a	n/a
2	RUNX3	chr5:70885613-70886184	GM12878	blood:	n/a	n/a
3	TCF3	chr5:70885818-70886084	GM12878	blood:	n/a	n/a
4	ZNF143	chr5:70885816-70886270	GM12878	blood:	n/a	n/a
5	RUNX3	chr5:70885669-70886131	GM12878	blood:	n/a	n/a
6	TCF12	chr5:70885771-70886051	GM12878	blood:	n/a	n/a
7	TCF3	chr5:70885720-70886165	GM12878	blood:	n/a	n/a
8	TCF12	chr5:70885763-70886041	GM12878	blood:	n/a	n/a
9	POLR2A	chr5:70885960-70885990	HepG2	liver:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:70881870..70884694-chr5:70885301..70891902,7	MCF-7	breast:
2	chr5:70881577..70886916-chr5:70891929..70900227,16	MCF-7	breast:
3	chr5:70870301..70875589-chr5:70883224..70887581,4	MCF-7	breast:
4	chr5:70882648..70886012-chr5:70920531..70924466,3	K562	blood:
5	chr5:70880133..70886735-chr5:70895650..70901637,10	MCF-7	breast:
6	chr5:70885597..70888590-chr5:70888980..70891724,4	MCF-7	breast:
7	chr5:70880665..70885311-chr5:70885640..70890340,6	K562	blood:
8	chr5:70883878..70887580-chr5:70891405..70894928,5	K562	blood:
9	chr5:70883251..70886427-chr5:70928765..70931034,4	MCF-7	breast:

No data

Variant related genes	Relation type
MCCC2	TF binding region
ENSG00000131844	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10044572	0.87[ASN][1000 genomes]
rs10071645	0.87[EUR][1000 genomes]
rs10073617	0.88[EUR][1000 genomes]
rs10077085	0.86[AMR][1000 genomes]
rs10434642	0.86[AMR][1000 genomes]
rs10474383	0.86[AMR][1000 genomes]
rs10805884	0.81[AMR][1000 genomes]
rs10942682	0.86[AMR][1000 genomes]
rs10942700	0.86[AMR][1000 genomes]
rs10942702	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10942705	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11746722	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12152748	0.83[ASN][1000 genomes]
rs12516456	1.00[CEU][hapmap];0.88[TSI][hapmap]
rs12652715	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13157835	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1553314	0.88[EUR][1000 genomes]
rs2270920	0.88[EUR][1000 genomes]
rs4062889	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4505929	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs62361818	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6452900	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6453014	0.85[ASN][1000 genomes]
rs6453035	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6453043	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6872671	0.86[AMR][1000 genomes]
rs6898471	0.86[AMR][1000 genomes]
rs715747	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7444180	0.88[EUR][1000 genomes]
rs7444322	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7446049	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7448422	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7449295	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7449316	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7714527	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7721179	0.83[ASN][1000 genomes]
rs9968768	0.81[AMR][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
rs12153571	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	chr5:70883800-70886000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr5:70883800-70889000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr5:70883800-70889800	Weak transcription	Lung	lung
4	chr5:70883800-70892000	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr5:70883800-70892000	Weak transcription	NH-A	brain
6	chr5:70883800-70895400	Weak transcription	HSMMtube	muscle
7	chr5:70883800-70896400	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr5:70883800-70906600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:70883800-70916400	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr5:70884000-70886200	Enhancers	Primary B cells from peripheral blood	blood
11	chr5:70884000-70886200	Enhancers	Pancreas	Pancrea
12	chr5:70884000-70886400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr5:70884000-70886600	Enhancers	Primary T cells fromperipheralblood	blood
14	chr5:70884000-70886600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr5:70884000-70887000	Enhancers	Adipose Nuclei	Adipose
16	chr5:70884000-70887800	Weak transcription	Fetal Stomach	stomach
17	chr5:70884000-70889800	Weak transcription	Fetal Muscle Trunk	muscle
18	chr5:70884000-70889800	Weak transcription	Fetal Muscle Leg	muscle
19	chr5:70884000-70891400	Weak transcription	Fetal Thymus	thymus
20	chr5:70884000-70891600	Weak transcription	Fetal Brain Female	brain
21	chr5:70884000-70892000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr5:70884000-70892000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr5:70884000-70892200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr5:70884000-70892400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr5:70884000-70892400	Weak transcription	Thymus	Thymus
26	chr5:70884000-70892800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr5:70884000-70892800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr5:70884000-70892800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr5:70884000-70893000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr5:70884000-70895400	Weak transcription	HSMM	muscle
31	chr5:70884000-70895400	Weak transcription	HUVEC	blood vessel
32	chr5:70884000-70896200	Weak transcription	Fetal Kidney	kidney
33	chr5:70884000-70896200	Weak transcription	NHDF-Ad	bronchial
34	chr5:70884000-70896200	Weak transcription	NHLF	lung
35	chr5:70884000-70900000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr5:70884200-70887000	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr5:70884200-70889000	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr5:70884200-70889200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr5:70884200-70893200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr5:70884400-70886000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr5:70884400-70886000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr5:70884400-70886200	Enhancers	Small Intestine	intestine
43	chr5:70884400-70886400	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr5:70884400-70889400	Weak transcription	Fetal Intestine Small	intestine
45	chr5:70884400-70892000	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr5:70884400-70892000	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr5:70884400-70892200	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr5:70884400-70892200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr5:70884400-70892200	Weak transcription	Fetal Intestine Large	intestine
50	chr5:70884600-70886000	Enhancers	Primary T cells from cord blood	blood

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