Variant report

Variant	rs28379847
Chromosome Location	chr2:47179063-47179064
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	chr2:47174154..47179572-chr2:47181486..47185069,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272814	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10168851	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11887744	1.00[ASN][1000 genomes]
rs13423962	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13432713	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17035813	0.87[ASN][1000 genomes]
rs17035823	0.87[ASN][1000 genomes]
rs17035919	1.00[ASN][1000 genomes]
rs2017797	1.00[ASN][1000 genomes]
rs59191871	1.00[ASN][1000 genomes]
rs6714269	1.00[ASN][1000 genomes]
rs7560422	1.00[ASN][1000 genomes]
rs7595101	1.00[ASN][1000 genomes]
rs9973504	0.86[EUR][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	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	nsv524970	chr2:47162739-47302095	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28379847	MCFD2	Cis_1M	lymphoblastoid	RTeQTL
rs28379847	MCFD2	cis	Artery Tibial	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47169600-47183600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr2:47169800-47182000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr2:47169800-47182200	Weak transcription	Right Ventricle	heart
4	chr2:47169800-47214600	Weak transcription	Fetal Kidney	kidney
5	chr2:47170000-47181600	Weak transcription	HUVEC	blood vessel
6	chr2:47170000-47182200	Weak transcription	Psoas Muscle	Psoas
7	chr2:47170200-47181400	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr2:47170800-47184000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr2:47171000-47182600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:47171200-47179400	Genic enhancers	Primary B cells from peripheral blood	blood
11	chr2:47171200-47182400	Weak transcription	Small Intestine	intestine
12	chr2:47171400-47179800	Genic enhancers	Primary monocytes fromperipheralblood	blood
13	chr2:47171400-47182000	Weak transcription	Colon Smooth Muscle	Colon
14	chr2:47171800-47181400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:47171800-47181400	Weak transcription	Right Atrium	heart
16	chr2:47173000-47191800	Weak transcription	Fetal Brain Male	brain
17	chr2:47173400-47181600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:47173400-47184000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr2:47173600-47179400	Genic enhancers	Primary B cells from cord blood	blood
20	chr2:47174000-47179200	Genic enhancers	Fetal Thymus	thymus
21	chr2:47174000-47182200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr2:47174200-47183800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr2:47174200-47184200	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr2:47174400-47212400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr2:47174800-47181400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:47175600-47181600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr2:47175800-47179400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
28	chr2:47176200-47181200	Strong transcription	Fetal Intestine Small	intestine
29	chr2:47176400-47192600	Strong transcription	Dnd41	blood
30	chr2:47177000-47179600	Strong transcription	Fetal Muscle Trunk	muscle
31	chr2:47177200-47179200	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
32	chr2:47177200-47180200	Strong transcription	Brain Cingulate Gyrus	brain
33	chr2:47177200-47180200	Strong transcription	Hela-S3	cervix
34	chr2:47177200-47181200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:47177200-47181800	Genic enhancers	A549	lung
36	chr2:47177200-47185000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr2:47177200-47210400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr2:47177400-47179200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr2:47177400-47180000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
40	chr2:47177400-47180200	Strong transcription	HepG2	liver
41	chr2:47177400-47180400	Strong transcription	Fetal Intestine Large	intestine
42	chr2:47177400-47180800	Strong transcription	Duodenum Mucosa	Duodenum
43	chr2:47177400-47180800	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr2:47177400-47181000	Strong transcription	Brain Angular Gyrus	brain
45	chr2:47177400-47182000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr2:47177400-47192800	Strong transcription	Fetal Stomach	stomach
47	chr2:47177600-47179400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr2:47177600-47179400	Strong transcription	Fetal Lung	lung
49	chr2:47177600-47179600	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr2:47177600-47179800	Strong transcription	Rectal Smooth Muscle	rectum

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