Variant report

Variant	rs7449316
Chromosome Location	chr5:70889870-70889871
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:70881870..70884694-chr5:70885301..70891902,7	MCF-7	breast:
2	chr5:70885597..70888590-chr5:70888980..70891724,4	MCF-7	breast:
3	chr5:70880665..70885311-chr5:70885640..70890340,6	K562	blood:

Variant related genes	Relation type
ENSG00000131844	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10055460	0.88[AFR][1000 genomes];0.84[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	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10434642	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10474383	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10805884	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs10942682	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10942700	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10942702	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs10942705	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs11746722	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs12152748	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12153571	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12516456	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[TSI][hapmap]
rs12652715	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13157835	0.97[AFR][1000 genomes];0.92[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	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs4505929	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs62361818	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6452900	0.84[AMR][1000 genomes]
rs6453018	0.85[ASN][1000 genomes]
rs6453035	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs6453043	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6872235	0.85[ASN][1000 genomes]
rs6872671	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6877773	0.85[ASN][1000 genomes]
rs6886336	0.85[ASN][1000 genomes]
rs6898471	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs715747	0.82[AFR][1000 genomes];0.87[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	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7446049	0.88[EUR][1000 genomes]
rs7448422	0.92[AMR][1000 genomes]
rs7449295	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7714527	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs9968768	0.84[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
rs7449316	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	chr5:70883800-70892000	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr5:70883800-70892000	Weak transcription	NH-A	brain
3	chr5:70883800-70895400	Weak transcription	HSMMtube	muscle
4	chr5:70883800-70896400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr5:70883800-70906600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:70883800-70916400	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr5:70884000-70891400	Weak transcription	Fetal Thymus	thymus
8	chr5:70884000-70891600	Weak transcription	Fetal Brain Female	brain
9	chr5:70884000-70892000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr5:70884000-70892000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr5:70884000-70892200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:70884000-70892400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr5:70884000-70892400	Weak transcription	Thymus	Thymus
14	chr5:70884000-70892800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr5:70884000-70892800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr5:70884000-70892800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr5:70884000-70893000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr5:70884000-70895400	Weak transcription	HSMM	muscle
19	chr5:70884000-70895400	Weak transcription	HUVEC	blood vessel
20	chr5:70884000-70896200	Weak transcription	Fetal Kidney	kidney
21	chr5:70884000-70896200	Weak transcription	NHDF-Ad	bronchial
22	chr5:70884000-70896200	Weak transcription	NHLF	lung
23	chr5:70884000-70900000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:70884200-70893200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr5:70884400-70892000	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr5:70884400-70892000	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr5:70884400-70892200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr5:70884400-70892200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr5:70884400-70892200	Weak transcription	Fetal Intestine Large	intestine
30	chr5:70884600-70891400	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr5:70884600-70892000	Weak transcription	Placenta	Placenta
32	chr5:70884600-70892000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr5:70884600-70892000	Weak transcription	Osteobl	bone
34	chr5:70884600-70892200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr5:70884600-70892200	Weak transcription	Fetal Lung	lung
36	chr5:70884600-70892200	Weak transcription	Rectal Smooth Muscle	rectum
37	chr5:70884600-70892400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr5:70884600-70892800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr5:70884600-70892800	Weak transcription	Brain Germinal Matrix	brain
40	chr5:70884600-70892800	Weak transcription	Esophagus	oesophagus
41	chr5:70884600-70906600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr5:70884800-70891400	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr5:70884800-70891600	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr5:70884800-70892000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr5:70884800-70892000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr5:70884800-70892000	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr5:70884800-70892200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr5:70884800-70892800	Weak transcription	Aorta	Aorta
49	chr5:70884800-70893200	Weak transcription	Colonic Mucosa	Colon
50	chr5:70884800-70896400	Weak transcription	Primary hematopoietic stem cells	blood

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