Variant report

Variant	rs6758512
Chromosome Location	chr2:47139183-47139184
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:47138983-47139270	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:47135393..47141252-chr2:47166022..47170880,5	K562	blood:
2	chr2:47137540..47139379-chr2:47400792..47403284,2	MCF-7	breast:
3	chr2:47137732..47140731-chr2:47403487..47405764,2	MCF-7	breast:
4	chr2:47127180..47130356-chr2:47136713..47140377,4	K562	blood:

Variant related genes	Relation type
MCFD2	TF binding region
TTC7A	TF binding region
ENSG00000068724	Chromatin interaction
ENSG00000143933	Chromatin interaction
ENSG00000180398	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10168851	0.92[EUR][1000 genomes]
rs10174894	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10199965	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11890177	0.94[ASN][1000 genomes]
rs11894319	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13388612	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13392448	0.91[ASN][1000 genomes]
rs13398851	0.83[ASN][1000 genomes]
rs13423962	0.87[EUR][1000 genomes]
rs1446499	0.96[ASN][1000 genomes]
rs1446500	0.96[ASN][1000 genomes]
rs17035859	0.84[ASN][1000 genomes]
rs17035867	0.88[ASN][1000 genomes]
rs17035884	0.94[ASN][1000 genomes]
rs17035887	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2084192	0.96[ASN][1000 genomes]
rs2289927	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2289928	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2347259	0.88[ASN][1000 genomes]
rs28516550	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3087857	0.96[ASN][1000 genomes]
rs34581142	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs35433380	1.00[ASN][1000 genomes]
rs4505575	0.80[ASN][1000 genomes]
rs55872217	1.00[ASN][1000 genomes]
rs56213467	0.92[ASN][1000 genomes]
rs58589709	0.91[ASN][1000 genomes]
rs60194846	0.96[ASN][1000 genomes]
rs61132855	0.88[ASN][1000 genomes]
rs62136818	0.84[ASN][1000 genomes]
rs62136819	0.84[ASN][1000 genomes]
rs62136820	0.88[ASN][1000 genomes]
rs62136822	0.94[ASN][1000 genomes]
rs62136823	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136825	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62136827	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62140550	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62140553	0.80[ASN][1000 genomes]
rs6544938	0.98[ASN][1000 genomes]
rs6544939	0.98[ASN][1000 genomes]
rs6706031	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6715391	0.94[ASN][1000 genomes]
rs6715620	0.96[ASN][1000 genomes]
rs6716381	0.96[ASN][1000 genomes]
rs6722440	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6729120	0.96[ASN][1000 genomes]
rs6729604	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6733548	0.96[ASN][1000 genomes]
rs6743966	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6743994	0.94[ASN][1000 genomes]
rs6745578	0.85[ASN][1000 genomes]
rs6755303	0.94[ASN][1000 genomes]
rs6758093	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71423929	0.96[ASN][1000 genomes]
rs7340475	0.88[ASN][1000 genomes]
rs73926966	0.96[ASN][1000 genomes]
rs754411	0.92[ASN][1000 genomes]
rs7565420	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7574514	0.84[ASN][1000 genomes]
rs7574833	0.86[ASN][1000 genomes]
rs7575172	0.96[ASN][1000 genomes]
rs7586004	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7596198	0.94[ASN][1000 genomes]
rs7601491	0.96[ASN][1000 genomes]
rs8861	0.94[ASN][1000 genomes]
rs9973504	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6758512	MCFD2	cis	Artery Tibial	GTEx
rs6758512	MCFD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47119600-47140800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:47129400-47140200	Strong transcription	Placenta	Placenta
3	chr2:47130600-47140800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:47131000-47139800	Strong transcription	Thymus	Thymus
5	chr2:47131000-47140000	Strong transcription	Fetal Intestine Large	intestine
6	chr2:47131000-47140200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr2:47131000-47140400	Strong transcription	Fetal Stomach	stomach
8	chr2:47131000-47140600	Strong transcription	Fetal Intestine Small	intestine
9	chr2:47131000-47140600	Strong transcription	Fetal Muscle Leg	muscle
10	chr2:47131200-47140400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:47131200-47141800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr2:47131400-47140200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr2:47131400-47142000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr2:47132200-47139600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr2:47133600-47141000	Weak transcription	Fetal Heart	heart
16	chr2:47134600-47139400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr2:47134800-47141000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr2:47135000-47141200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr2:47135200-47140600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr2:47135200-47140800	Weak transcription	Small Intestine	intestine
21	chr2:47136000-47139800	Weak transcription	Psoas Muscle	Psoas
22	chr2:47136000-47140800	Weak transcription	Fetal Brain Male	brain
23	chr2:47136400-47140600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr2:47136400-47140800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr2:47136600-47140400	Genic enhancers	HepG2	liver
26	chr2:47136800-47141000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr2:47136800-47141800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr2:47137000-47139800	Weak transcription	Brain Hippocampus Middle	brain
29	chr2:47137200-47139600	Weak transcription	Colon Smooth Muscle	Colon
30	chr2:47137200-47140600	Weak transcription	Aorta	Aorta
31	chr2:47137200-47141000	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr2:47137200-47141200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr2:47137200-47142000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr2:47137400-47139800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr2:47137400-47140000	Weak transcription	Brain Anterior Caudate	brain
36	chr2:47137400-47140000	Strong transcription	Stomach Smooth Muscle	stomach
37	chr2:47137400-47140600	Weak transcription	Right Atrium	heart
38	chr2:47137400-47140600	Weak transcription	HSMMtube	muscle
39	chr2:47137600-47139600	Weak transcription	Fetal Lung	lung
40	chr2:47137600-47139800	Weak transcription	Stomach Mucosa	stomach
41	chr2:47137600-47140400	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr2:47137600-47140400	Weak transcription	GM12878-XiMat	blood
43	chr2:47137600-47140600	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr2:47137600-47140800	Weak transcription	Brain Cingulate Gyrus	brain
45	chr2:47137600-47141000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr2:47137600-47141000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr2:47137600-47141200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr2:47137800-47139400	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr2:47137800-47139600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr2:47137800-47139600	Weak transcription	NHDF-Ad	bronchial

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