Variant report

Variant	rs6888301
Chromosome Location	chr5:70948385-70948386
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:70941935..70943473-chr5:70947119..70949979,2	MCF-7	breast:
2	chr5:70947206..70949359-chr5:71011113..71012653,2	K562	blood:

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10058683	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10064079	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10065732	0.80[EUR][1000 genomes]
rs10805891	0.88[EUR][1000 genomes]
rs1135667	1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1391180	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2242372	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6453080	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6875115	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7731970	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[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
rs6888301	MCCC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:70898400-70955000	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr5:70898600-70948400	Weak transcription	Brain Germinal Matrix	brain
3	chr5:70906600-70952400	Weak transcription	Stomach Mucosa	stomach
4	chr5:70914200-70948800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:70915400-70950800	Weak transcription	NHLF	lung
6	chr5:70919800-70955000	Weak transcription	HUVEC	blood vessel
7	chr5:70925400-70950600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr5:70926600-70954000	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr5:70927000-70954000	Strong transcription	Dnd41	blood
10	chr5:70927000-70954200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr5:70930400-70952600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr5:70931400-70953600	Weak transcription	HSMM	muscle
13	chr5:70934800-70953800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr5:70935000-70955800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr5:70935600-70948600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr5:70936600-70955200	Weak transcription	Fetal Heart	heart
17	chr5:70938400-70954000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr5:70938600-70948400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr5:70939400-70948600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr5:70940800-70954600	Strong transcription	Liver	Liver
21	chr5:70941000-70950000	Strong transcription	Primary B cells from peripheral blood	blood
22	chr5:70941000-70951400	Strong transcription	Fetal Intestine Large	intestine
23	chr5:70941200-70955000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr5:70941400-70950000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr5:70941400-70950000	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr5:70941400-70950200	Strong transcription	Skeletal Muscle Female	skeletal muscle
27	chr5:70941400-70954200	Strong transcription	Placenta	Placenta
28	chr5:70941400-70954400	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr5:70941400-70954400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr5:70941400-70954600	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr5:70941400-70954600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr5:70941600-70948800	Strong transcription	Left Ventricle	heart
33	chr5:70941600-70949000	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr5:70941600-70954400	Strong transcription	Duodenum Mucosa	Duodenum
35	chr5:70941600-70954600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr5:70942000-70948800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr5:70942000-70949400	Strong transcription	HepG2	liver
38	chr5:70942000-70949800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr5:70942000-70950000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr5:70942000-70950200	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr5:70942000-70951600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr5:70942000-70954400	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr5:70942000-70954400	Strong transcription	Adipose Nuclei	Adipose
44	chr5:70942000-70954400	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr5:70942200-70949600	Strong transcription	Fetal Muscle Leg	muscle
46	chr5:70942200-70949800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr5:70942200-70950200	Strong transcription	Fetal Intestine Small	intestine
48	chr5:70942200-70953800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr5:70942200-70954000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr5:70942200-70954200	Strong transcription	Fetal Muscle Trunk	muscle

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