Variant report

Variant	rs6871148
Chromosome Location	chr5:70920501-70920502
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10044572	0.85[AFR][1000 genomes]
rs10055460	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10060578	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10064099	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10077085	0.87[ASN][1000 genomes]
rs10434642	0.84[ASN][1000 genomes]
rs10474383	0.84[ASN][1000 genomes]
rs10942682	0.84[ASN][1000 genomes]
rs10942700	0.87[ASN][1000 genomes]
rs12516456	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6453018	0.84[ASN][1000 genomes]
rs6872235	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6872671	0.84[ASN][1000 genomes]
rs6877773	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6886336	0.84[ASN][1000 genomes]
rs6898471	0.84[ASN][1000 genomes]
rs7378662	0.84[ASN][1000 genomes]
rs7380115	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs7380280	0.84[ASN][1000 genomes]
rs9968768	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6871148	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	chr5:70897000-70925800	Weak transcription	Right Ventricle	heart
5	chr5:70897200-70930000	Weak transcription	Psoas Muscle	Psoas
6	chr5:70897400-70921000	Weak transcription	Fetal Heart	heart
7	chr5:70897400-70933800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr5:70897800-70944800	Weak transcription	Small Intestine	intestine
9	chr5:70898200-70944200	Weak transcription	Osteobl	bone
10	chr5:70898400-70935400	Weak transcription	NHDF-Ad	bronchial
11	chr5:70898400-70955000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr5:70898600-70922400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr5:70898600-70948400	Weak transcription	Brain Germinal Matrix	brain
14	chr5:70900000-70944800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr5:70900200-70925800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:70900200-70928200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr5:70900200-70930800	Weak transcription	HMEC	breast
18	chr5:70900200-70945200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr5:70900400-70922800	Weak transcription	Fetal Kidney	kidney
20	chr5:70900400-70927000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr5:70900400-70927600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr5:70900400-70927800	Weak transcription	Brain Substantia Nigra	brain
23	chr5:70900400-70931000	Weak transcription	K562	blood
24	chr5:70900400-70933200	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr5:70906600-70923400	Strong transcription	Primary T cells from cord blood	blood
26	chr5:70906600-70952400	Weak transcription	Stomach Mucosa	stomach
27	chr5:70906800-70923400	Strong transcription	Liver	Liver
28	chr5:70907200-70927000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr5:70907200-70928200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr5:70907400-70932800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr5:70907600-70928000	Weak transcription	Fetal Lung	lung
32	chr5:70908800-70927200	Weak transcription	Thymus	Thymus
33	chr5:70909000-70938200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr5:70909200-70931000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr5:70911200-70928000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr5:70912200-70931000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr5:70912400-70922800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr5:70912400-70927000	Weak transcription	Brain Angular Gyrus	brain
39	chr5:70912400-70936600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr5:70912600-70927800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr5:70912600-70941800	Weak transcription	Colon Smooth Muscle	Colon
42	chr5:70912600-70943800	Weak transcription	A549	lung
43	chr5:70912800-70922800	Weak transcription	HSMM	muscle
44	chr5:70912800-70927000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr5:70913000-70922400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr5:70913000-70927000	Weak transcription	Pancreas	Pancrea
47	chr5:70913000-70928000	Weak transcription	Brain Anterior Caudate	brain
48	chr5:70913000-70934200	Weak transcription	Fetal Brain Female	brain
49	chr5:70913200-70927000	Weak transcription	NHEK	skin
50	chr5:70913200-70928200	Weak transcription	Brain Cingulate Gyrus	brain

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