Variant report

Variant	rs10060578
Chromosome Location	chr5:70928448-70928449
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:70924678..70928515-chr5:71047455..71049125,3	MCF-7	breast:
2	chr5:70829837..70831785-chr5:70927943..70929990,2	MCF-7	breast:
3	chr5:70926856..70929109-chr5:70934806..70937462,2	MCF-7	breast:
4	chr5:70920053..70922603-chr5:70926278..70929720,3	K562	blood:

Variant related genes	Relation type
ENSG00000131844	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10044572	0.85[EUR][1000 genomes]
rs10055460	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10064099	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10071645	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10073617	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10077085	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10434642	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10474383	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10805884	0.83[EUR][1000 genomes]
rs10942682	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10942700	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10942702	0.85[EUR][1000 genomes]
rs10942705	0.83[EUR][1000 genomes]
rs11746722	0.85[EUR][1000 genomes]
rs12152748	0.84[EUR][1000 genomes]
rs12516456	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13157835	0.85[EUR][1000 genomes]
rs1553314	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2270920	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4062889	0.85[EUR][1000 genomes]
rs4505929	0.85[EUR][1000 genomes]
rs6453014	0.81[EUR][1000 genomes]
rs6453018	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6453035	0.85[EUR][1000 genomes]
rs6871148	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6872235	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6872671	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6877773	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6886336	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6898471	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs715747	0.81[EUR][1000 genomes]
rs7378662	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7380115	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7380280	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7444180	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7448422	0.81[EUR][1000 genomes]
rs7721179	0.81[EUR][1000 genomes]
rs9968768	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
3	nsv532805	chr5:70916228-71020967	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv933076	chr5:70927790-70931298	ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv933359	chr5:70927969-70931298	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10060578	MCCC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:70884800-70934800	Weak transcription	Fetal Brain Male	brain
2	chr5:70893600-70930200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr5:70895800-70937800	Weak transcription	Colonic Mucosa	Colon
4	chr5:70897200-70930000	Weak transcription	Psoas Muscle	Psoas
5	chr5:70897400-70933800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr5:70897800-70944800	Weak transcription	Small Intestine	intestine
7	chr5:70898200-70944200	Weak transcription	Osteobl	bone
8	chr5:70898400-70935400	Weak transcription	NHDF-Ad	bronchial
9	chr5:70898400-70955000	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr5:70898600-70948400	Weak transcription	Brain Germinal Matrix	brain
11	chr5:70900000-70944800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr5:70900200-70930800	Weak transcription	HMEC	breast
13	chr5:70900200-70945200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr5:70900400-70931000	Weak transcription	K562	blood
15	chr5:70900400-70933200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr5:70906600-70952400	Weak transcription	Stomach Mucosa	stomach
17	chr5:70907400-70932800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr5:70909000-70938200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr5:70909200-70931000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr5:70912200-70931000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr5:70912400-70936600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr5:70912600-70941800	Weak transcription	Colon Smooth Muscle	Colon
23	chr5:70912600-70943800	Weak transcription	A549	lung
24	chr5:70913000-70934200	Weak transcription	Fetal Brain Female	brain
25	chr5:70914200-70930400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr5:70914200-70938000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr5:70914200-70948800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:70915400-70950800	Weak transcription	NHLF	lung
29	chr5:70917000-70936400	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr5:70917000-70945000	Weak transcription	Hela-S3	cervix
31	chr5:70917200-70930000	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr5:70917200-70937800	Weak transcription	Aorta	Aorta
33	chr5:70917200-70942000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr5:70917400-70942600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr5:70918000-70942400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr5:70919400-70934800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr5:70919800-70930000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr5:70919800-70930200	Weak transcription	HSMMtube	muscle
39	chr5:70919800-70955000	Weak transcription	HUVEC	blood vessel
40	chr5:70920200-70930200	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr5:70920200-70932200	Weak transcription	Fetal Intestine Small	intestine
42	chr5:70923200-70936400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr5:70923200-70937600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr5:70923400-70930400	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr5:70923400-70930800	Weak transcription	Fetal Kidney	kidney
46	chr5:70923600-70930200	Weak transcription	HSMM	muscle
47	chr5:70925400-70950600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr5:70925800-70928600	Enhancers	Fetal Heart	heart
49	chr5:70925800-70929400	Strong transcription	Primary B cells from cord blood	blood
50	chr5:70926200-70930200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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