Variant report

Variant	rs62140549
Chromosome Location	chr2:47141965-47141966
allele	A/G
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	chr2:47141959-47143510	K562	blood:	n/a	n/a
2	USF1	chr2:47141861-47142533	K562	blood:	n/a	chr2:47142152-47142163
3	POLR2A	chr2:47140623-47143684	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr2:47140983-47143666	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr2:47141125-47143537	U87	brain:	n/a	n/a
6	POLR2A	chr2:47140644-47144305	IMR90	lung:	n/a	n/a
7	MXI1	chr2:47140343-47144102	SK-N-SH	brain:	n/a	n/a
8	USF1	chr2:47141781-47142473	HCT-116	colon:	n/a	chr2:47142152-47142163
9	NR2F2	chr2:47140589-47142411	K562	blood:	n/a	n/a
10	USF1	chr2:47141894-47142449	SK-N-SH	brain:	n/a	chr2:47142152-47142163
11	USF1	chr2:47141935-47142358	K562	blood:	n/a	chr2:47142152-47142163
12	USF2	chr2:47141930-47142334	Hela-S3	cervix:	n/a	chr2:47142152-47142163
13	POLR2A	chr2:47140962-47143816	U87	brain:	n/a	n/a
14	MAX	chr2:47141957-47142326	K562	blood:	n/a	n/a
15	POLR2A	chr2:47141209-47143627	MCF10A-Er-Src	breast:	n/a	n/a
16	MAZ	chr2:47141928-47143798	IMR90	lung:	n/a	n/a
17	POLR2A	chr2:47139505-47143657	K562	blood:	n/a	n/a
18	USF1	chr2:47141888-47142423	A549	lung:	n/a	chr2:47142152-47142163
19	USF1	chr2:47141918-47142403	ECC-1	luminal epithelium:	n/a	chr2:47142152-47142163
20	POLR2A	chr2:47140684-47143537	U87	brain:	n/a	n/a
21	MXI1	chr2:47140686-47144024	IMR90	lung:	n/a	n/a
22	POLR2A	chr2:47140962-47143692	U87	brain:	n/a	n/a
23	POLR2A	chr2:47140800-47143659	PBDE	blood:	n/a	n/a
24	BCL3	chr2:47141838-47143819	A549	lung:	n/a	n/a
25	USF1	chr2:47141960-47142330	HepG2	liver:	n/a	chr2:47142152-47142163
26	USF1	chr2:47141939-47142423	H1-hESC	embryonic stem cell:	n/a	chr2:47142152-47142163
27	IRF1	chr2:47141819-47142403	K562	blood:	n/a	n/a
28	USF1	chr2:47141941-47142296	SK-N-SH_RA	brain:	n/a	chr2:47142152-47142163
29	USF1	chr2:47141861-47142341	A549	lung:	n/a	chr2:47142152-47142163
30	POLR2A	chr2:47141887-47142366	HUVEC	blood vessel:	n/a	n/a
31	USF1	chr2:47141914-47142370	A549	lung:	n/a	chr2:47142152-47142163
32	RCOR1	chr2:47141922-47141992	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:46843200..46845178-chr2:47140240..47142665,2	MCF-7	breast:
2	chr2:47141053..47143152-chr2:47167792..47169429,2	MCF-7	breast:
3	chr2:47124791..47126601-chr2:47141320..47142897,2	K562	blood:
4	chr2:47141013..47143779-chr2:47401317..47404567,3	MCF-7	breast:
5	chr2:47140743..47148534-chr2:47401019..47406419,10	MCF-7	breast:
6	chr2:47139463..47143529-chr2:47167839..47169953,4	K562	blood:
7	chr2:47140015..47142269-chr2:47400720..47402759,3	K562	blood:
8	chr2:47140015..47142222-chr2:47401259..47403402,2	K562	blood:
9	chr2:47139886..47146981-chr2:47165365..47170438,17	MCF-7	breast:
10	chr2:47141557..47143529-chr2:47167839..47169788,2	K562	blood:

Variant related genes	Relation type
TTC7A	TF binding region
MCFD2	TF binding region
ENSG00000151665	Chromatin interaction
ENSG00000068724	Chromatin interaction
ENSG00000143933	Chromatin interaction
ENSG00000119878	Chromatin interaction
ENSG00000180398	Chromatin interaction
ENSG00000228925	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1051317	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12621059	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2117168	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6419615	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6544941	0.85[EUR][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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47131400-47142000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:47137200-47142000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:47139800-47142200	Enhancers	Sigmoid Colon	Sigmoid Colon
4	chr2:47140400-47142000	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr2:47140400-47142000	Enhancers	Placenta Amnion	Placenta Amnion
6	chr2:47140400-47142000	Flanking Active TSS	NH-A	brain
7	chr2:47140400-47142200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
8	chr2:47140400-47142400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:47140600-47142000	Enhancers	Primary T cells fromperipheralblood	blood
10	chr2:47140600-47142000	Enhancers	Gastric	stomach
11	chr2:47140600-47142200	Enhancers	Spleen	Spleen
12	chr2:47140600-47142200	Flanking Active TSS	HMEC	breast
13	chr2:47140600-47142400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:47140600-47142400	Flanking Active TSS	HUVEC	blood vessel
15	chr2:47140600-47144400	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr2:47140800-47142000	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr2:47140800-47142000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr2:47140800-47142000	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr2:47140800-47142000	Flanking Active TSS	HSMM	muscle
20	chr2:47140800-47142400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr2:47140800-47142400	Flanking Active TSS	Liver	Liver
22	chr2:47140800-47142400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr2:47140800-47142400	Enhancers	Small Intestine	intestine
24	chr2:47140800-47142600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr2:47140800-47142600	Flanking Active TSS	Adipose Nuclei	Adipose
26	chr2:47141000-47142000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:47141000-47142000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr2:47141000-47142000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr2:47141000-47142000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
30	chr2:47141000-47142000	Flanking Active TSS	GM12878-XiMat	blood
31	chr2:47141000-47142200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr2:47141000-47142200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr2:47141000-47142200	Enhancers	Primary B cells from peripheral blood	blood
34	chr2:47141000-47142200	Flanking Active TSS	Brain Cingulate Gyrus	brain
35	chr2:47141000-47142200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr2:47141000-47142200	Flanking Active TSS	Stomach Mucosa	stomach
37	chr2:47141000-47142400	Flanking Active TSS	Brain Hippocampus Middle	brain
38	chr2:47141000-47142400	Flanking Active TSS	Duodenum Mucosa	Duodenum
39	chr2:47141000-47142400	Flanking Active TSS	Hela-S3	cervix
40	chr2:47141000-47142400	Flanking Active TSS	Osteobl	bone
41	chr2:47141000-47142600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr2:47141200-47142000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr2:47141200-47142000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr2:47141200-47142000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr2:47141200-47142000	Enhancers	Esophagus	oesophagus
46	chr2:47141200-47142000	Flanking Active TSS	HSMMtube	muscle
47	chr2:47141200-47142200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr2:47141200-47142200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr2:47141200-47142200	Flanking Active TSS	Fetal Heart	heart
50	chr2:47141200-47142400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links