Variant report

Variant	rs6453043
Chromosome Location	chr5:70892486-70892487
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	chr5:70881577..70886916-chr5:70891929..70900227,16	MCF-7	breast:
2	chr5:70882161..70884487-chr5:70891024..70893721,4	MCF-7	breast:

Variant related genes	Relation type
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	0.85[ASN][1000 genomes]
rs10055460	0.84[AMR][1000 genomes]
rs10071645	0.86[EUR][1000 genomes]
rs10073617	0.88[EUR][1000 genomes]
rs10077085	0.92[AMR][1000 genomes]
rs10434642	0.92[AMR][1000 genomes]
rs10474383	0.92[AMR][1000 genomes]
rs10805884	0.87[AMR][1000 genomes]
rs10942682	0.92[AMR][1000 genomes]
rs10942700	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs10942702	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10942705	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11746722	0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12152748	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12153571	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12652715	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13157835	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1553314	0.87[EUR][1000 genomes]
rs2270920	0.87[EUR][1000 genomes]
rs4062889	0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4505929	0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62361818	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6452900	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6453014	0.84[ASN][1000 genomes]
rs6453035	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6872671	0.92[AMR][1000 genomes]
rs6898471	0.92[AMR][1000 genomes]
rs715747	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7444180	0.87[EUR][1000 genomes]
rs7444322	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7446049	0.88[EUR][1000 genomes]
rs7448422	0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7449295	0.89[EUR][1000 genomes]
rs7449316	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7714527	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7721179	0.82[ASN][1000 genomes]
rs9968768	0.84[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
rs6453043	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	chr5:70883800-70895400	Weak transcription	HSMMtube	muscle
2	chr5:70883800-70896400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr5:70883800-70906600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:70883800-70916400	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr5:70884000-70892800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:70884000-70892800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr5:70884000-70892800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr5:70884000-70893000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr5:70884000-70895400	Weak transcription	HSMM	muscle
10	chr5:70884000-70895400	Weak transcription	HUVEC	blood vessel
11	chr5:70884000-70896200	Weak transcription	Fetal Kidney	kidney
12	chr5:70884000-70896200	Weak transcription	NHDF-Ad	bronchial
13	chr5:70884000-70896200	Weak transcription	NHLF	lung
14	chr5:70884000-70900000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:70884200-70893200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr5:70884600-70892800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr5:70884600-70892800	Weak transcription	Brain Germinal Matrix	brain
18	chr5:70884600-70892800	Weak transcription	Esophagus	oesophagus
19	chr5:70884600-70906600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr5:70884800-70892800	Weak transcription	Aorta	Aorta
21	chr5:70884800-70893200	Weak transcription	Colonic Mucosa	Colon
22	chr5:70884800-70896400	Weak transcription	Primary hematopoietic stem cells	blood
23	chr5:70884800-70896400	Weak transcription	Stomach Mucosa	stomach
24	chr5:70884800-70934800	Weak transcription	Fetal Brain Male	brain
25	chr5:70885000-70893200	Weak transcription	Colon Smooth Muscle	Colon
26	chr5:70885200-70896400	Weak transcription	Fetal Heart	heart
27	chr5:70885200-70899600	Weak transcription	Brain Substantia Nigra	brain
28	chr5:70885400-70893000	Weak transcription	HMEC	breast
29	chr5:70885400-70896600	Weak transcription	Psoas Muscle	Psoas
30	chr5:70885400-70896600	Weak transcription	K562	blood
31	chr5:70885400-70899800	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr5:70885600-70892800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr5:70885800-70896600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr5:70886000-70893200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr5:70886200-70892800	Weak transcription	Pancreas	Pancrea
36	chr5:70886200-70896600	Weak transcription	Small Intestine	intestine
37	chr5:70886400-70894800	Weak transcription	GM12878-XiMat	blood
38	chr5:70887000-70896400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr5:70888400-70896000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr5:70888600-70900400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr5:70888600-70901000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr5:70888800-70896400	Strong transcription	Liver	Liver
43	chr5:70889000-70897000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr5:70889200-70895600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr5:70889600-70896200	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr5:70889600-70896400	Strong transcription	Dnd41	blood
47	chr5:70889600-70896600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr5:70889800-70895600	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr5:70889800-70900000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr5:70890200-70894200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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