Variant report

Variant	rs1376405
Chromosome Location	chr2:46768543-46768544
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:6)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:23 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr2:46767603-46770001	SK-N-SH	brain:	n/a	chr2:46768518-46768527 chr2:46767833-46767842
2	EP300	chr2:46766289-46769972	SK-N-SH	brain:	n/a	chr2:46769660-46769673
3	CTCF	chr2:46768520-46768670	HEEpiC	esophagus:	n/a	n/a
4	REST	chr2:46767643-46769926	H1-neurons	neurons:	n/a	chr2:46769603-46769623
5	SMC3	chr2:46767616-46770132	SK-N-SH	brain:	n/a	n/a
6	ATF3	chr2:46768493-46769183	A549	lung:	n/a	n/a
7	CTCF	chr2:46768460-46768610	GM12867	blood:	n/a	n/a
8	TCF12	chr2:46768182-46769838	A549	lung:	n/a	n/a
9	JUN	chr2:46767714-46768570	K562	blood:	n/a	chr2:46768518-46768527 chr2:46767983-46767996 chr2:46767833-46767842
10	MAZ	chr2:46767582-46771842	IMR90	lung:	n/a	chr2:46770978-46770988 chr2:46771602-46771613
11	MAX	chr2:46768539-46769911	A549	lung:	n/a	n/a
12	POLR2A	chr2:46768516-46769955	Raji	blood:	n/a	n/a
13	MXI1	chr2:46768510-46771730	IMR90	lung:	n/a	n/a
14	CTBP2	chr2:46768503-46769634	H1-hESC	embryonic stem cell:	n/a	n/a
15	CTCF	chr2:46767584-46769778	A549	lung:	n/a	n/a
16	SMARCC1	chr2:46767660-46769509	Hela-S3	cervix:	n/a	n/a
17	CTCF	chr2:46768045-46769933	SK-N-SH	brain:	n/a	n/a
18	MXI1	chr2:46766247-46772861	SK-N-SH	brain:	n/a	n/a
19	MTA3	chr2:46768279-46769719	GM12878	blood:	n/a	n/a
20	RCOR1	chr2:46767643-46769892	IMR90	lung:	n/a	n/a
21	CTCF	chr2:46768540-46768690	MCF-7	breast:	n/a	n/a
22	RAD21	chr2:46768250-46769936	SK-N-SH	brain:	n/a	chr2:46769854-46769867
23	SP1	chr2:46768426-46769742	A549	lung:	n/a	chr2:46769625-46769639

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:46767796..46769414-chr2:46769669..46772927,3	MCF-7	breast:
2	chr2:46768098..46772914-chr2:46841294..46848059,11	K562	blood:
3	chr2:46726104..46727862-chr2:46768328..46770840,3	MCF-7	breast:
4	chr2:46721184..46729524-chr2:46766976..46775977,14	K562	blood:
5	chr2:46768338..46773881-chr2:46842376..46848059,6	K562	blood:
6	chr2:46768345..46771564-chr2:46842518..46844841,5	MCF-7	breast:
7	chr2:46661070..46664987-chr2:46768132..46770822,3	K562	blood:

(count:6 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ATP6V1E2-5	chr2:46768529-46768592	NONHSAT070501
2	lnc-ATP6V1E2-5	chr2:46768529-46769141	NONHSAT070508
3	lnc-ATP6V1E2-5	chr2:46768529-46768728	NONHSAT070510
4	lnc-ATP6V1E2-5	chr2:46768530-46768722	NONHSAT070507
5	lnc-ATP6V1E2-5	chr2:46768529-46768722	NONHSAT070506
6	lnc-RHOQ-2	chr2:46768529-46768609	NONHSAT070509

No data

Variant related genes	Relation type
RHOQ	TF binding region
ENSG00000250565	Chromatin interaction
ENSG00000187600	Chromatin interaction
ENSG00000119878	Chromatin interaction
ENSG00000119729	Chromatin interaction
ENSG00000253515	Chromatin interaction
ENSG00000151665	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs2053900	0.93[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs3754552	0.82[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4952832	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6714484	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6747288	0.86[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7565377	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7568909	0.88[CHB][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv34650	chr2:46605659-46818992	Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv34937	chr2:46651624-46818586	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv1009735	chr2:46724523-46913152	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	esv3422495	chr2:46761899-46769356	Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1376405	LOC728819	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46761200-46768600	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr2:46761200-46768800	Enhancers	Primary B cells from peripheral blood	blood
3	chr2:46762600-46768600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:46763200-46768600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr2:46763600-46768600	Weak transcription	Liver	Liver
6	chr2:46765200-46768800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:46765200-46768800	Enhancers	NHDF-Ad	bronchial
8	chr2:46765400-46768600	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr2:46766400-46768600	Enhancers	Adipose Nuclei	Adipose
10	chr2:46766400-46768800	Enhancers	Fetal Muscle Leg	muscle
11	chr2:46766400-46768800	Enhancers	Fetal Thymus	thymus
12	chr2:46766400-46768800	Enhancers	Left Ventricle	heart
13	chr2:46766600-46768600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:46766600-46768600	Enhancers	Fetal Heart	heart
15	chr2:46766800-46768600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:46766800-46768600	Enhancers	Fetal Stomach	stomach
17	chr2:46766800-46768600	Enhancers	NH-A	brain
18	chr2:46767000-46768600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr2:46767000-46768800	Enhancers	NHLF	lung
20	chr2:46767200-46768600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr2:46767200-46768800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr2:46767200-46769200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:46767400-46768800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr2:46767600-46768600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr2:46767600-46768600	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr2:46767600-46768800	Enhancers	HSMMtube	muscle
27	chr2:46767800-46768600	Enhancers	Muscle Satellite Cultured Cells	--
28	chr2:46767800-46768600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:46767800-46768600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr2:46767800-46768600	Enhancers	Fetal Intestine Small	intestine
31	chr2:46767800-46768600	Enhancers	Fetal Lung	lung
32	chr2:46767800-46768600	Enhancers	Pancreas	Pancrea
33	chr2:46767800-46768600	Enhancers	HSMM	muscle
34	chr2:46767800-46768600	Enhancers	HUVEC	blood vessel
35	chr2:46767800-46768600	Enhancers	NHEK	skin
36	chr2:46767800-46768800	Enhancers	Placenta	Placenta
37	chr2:46767800-46768800	Enhancers	Psoas Muscle	Psoas
38	chr2:46767800-46768800	Enhancers	Stomach Mucosa	stomach
39	chr2:46767800-46769200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
40	chr2:46767800-46769400	Flanking Active TSS	Stomach Smooth Muscle	stomach
41	chr2:46768000-46768600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
42	chr2:46768000-46768600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
43	chr2:46768000-46768600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr2:46768000-46768600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
45	chr2:46768000-46768600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr2:46768000-46768600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
47	chr2:46768000-46768600	Enhancers	Fetal Brain Male	brain
48	chr2:46768000-46768600	Enhancers	Fetal Intestine Large	intestine
49	chr2:46768000-46768600	Enhancers	HMEC	breast
50	chr2:46768000-46768800	Enhancers	Placenta Amnion	Placenta Amnion

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