Variant report

Variant	rs13404012
Chromosome Location	chr2:99795845-99795846
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:185)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:185 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr2:99795720-99795870	HEK293	kidney:	n/a	n/a
2	RAD21	chr2:99795610-99795868	K562	blood:	n/a	n/a
3	CTCF	chr2:99795720-99795870	HBMEC	blood vessel:	n/a	n/a
4	CTCF	chr2:99795693-99795914	GM13977	blood:	n/a	n/a
5	CTCF	chr2:99795580-99796020	GM12878	blood:	n/a	n/a
6	CTCF	chr2:99795720-99795870	HCFaa	heart:	n/a	n/a
7	RAD21	chr2:99795477-99796050	MCF-7	breast:	n/a	n/a
8	NRF1	chr2:99795641-99795888	GM12878	blood:	n/a	n/a
9	CTCF	chr2:99795740-99795890	HMEC	breast:	n/a	n/a
10	CTCF	chr2:99795700-99795850	SAEC	small airway:	n/a	n/a
11	CTCF	chr2:99795760-99795910	RPTEC	kidney:	n/a	n/a
12	RAD21	chr2:99795618-99795943	A549	lung:	n/a	n/a
13	RAD21	chr2:99795587-99795973	HepG2	liver:	n/a	n/a
14	CTCF	chr2:99795618-99795983	K562	blood:	n/a	n/a
15	IRF4	chr2:99795564-99795890	GM12878	blood:	n/a	n/a
16	ZNF143	chr2:99795629-99795969	H1-hESC	embryonic stem cell:	n/a	n/a
17	CTCF	chr2:99795720-99795870	SAEC	small airway:	n/a	n/a
18	CTCF	chr2:99795720-99795870	GM12869	blood:	n/a	n/a
19	MAX	chr2:99795753-99795951	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr2:99795705-99795923	A549	lung:	n/a	n/a
21	CTCF	chr2:99795694-99795902	NHEK	skin:	n/a	n/a
22	CTCF	chr2:99795687-99795893	Fibrobl	skin:	n/a	n/a
23	CTCF	chr2:99795780-99795930	GM12873	blood:	n/a	n/a
24	CTCF	chr2:99795700-99795850	HPF	lung:	n/a	n/a
25	ZNF384	chr2:99795605-99795935	K562	blood:	n/a	n/a
26	CTCF	chr2:99795700-99795850	GM06990	blood:	n/a	n/a
27	CTCF	chr2:99795638-99795996	H1-hESC	embryonic stem cell:	n/a	n/a
28	CTCF	chr2:99795704-99795922	HepG2	liver:	n/a	n/a
29	ZNF143	chr2:99795638-99795971	K562	blood:	n/a	n/a
30	CTCF	chr2:99795740-99795890	GM12875	blood:	n/a	n/a
31	RAD21	chr2:99795637-99795973	IMR90	lung:	n/a	n/a
32	CTCF	chr2:99795720-99795870	NB4	blood:	n/a	n/a
33	RAD21	chr2:99795524-99796012	A549	lung:	n/a	n/a
34	CTCF	chr2:99795700-99795850	AG09309	skin:	n/a	n/a
35	CTCF	chr2:99795760-99795910	HCT-116	colon:	n/a	n/a
36	RAD21	chr2:99795505-99796086	A549	lung:	n/a	n/a
37	CTCF	chr2:99795700-99795850	HCPEpiC	choroid plexus:	n/a	n/a
38	CTCF	chr2:99795700-99795850	MCF-7	breast:	n/a	n/a
39	EP300	chr2:99795631-99795896	GM12878	blood:	n/a	n/a
40	CTCF	chr2:99795621-99795957	K562	blood:	n/a	n/a
41	CTCF	chr2:99795633-99795928	MCF-7	breast:	n/a	n/a
42	CTCF	chr2:99795679-99795919	MCF-7	breast:	n/a	n/a
43	CTCF	chr2:99795760-99795910	GM12873	blood:	n/a	n/a
44	TBL1XR1	chr2:99795650-99795989	GM12878	blood:	n/a	n/a
45	CTCF	chr2:99795740-99795890	RPTEC	kidney:	n/a	n/a
46	CTCF	chr2:99795700-99795850	GM12864	blood:	n/a	n/a
47	CTCF	chr2:99795740-99795890	GM12872	blood:	n/a	n/a
48	ARID3A	chr2:99795686-99795946	HepG2	liver:	n/a	n/a
49	CTCF	chr2:99795675-99795897	A549	lung:	n/a	n/a
50	WRNIP1	chr2:99795647-99795944	GM12878	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:99782491..99787778-chr2:99795073..99800536,8	MCF-7	breast:
2	chr2:99767297..99778137-chr2:99793643..99800044,16	MCF-7	breast:
3	chr2:99785439..99787050-chr2:99795016..99797039,2	MCF-7	breast:
4	chr2:99773460..99775847-chr2:99795647..99797318,2	K562	blood:
5	chr2:99757575..99760395-chr2:99795675..99798209,3	K562	blood:
6	chr2:99767233..99772869-chr2:99793831..99799744,8	K562	blood:
7	chr2:99769587..99774574-chr2:99795787..99799597,12	MCF-7	breast:
8	chr2:99755178..99760444-chr2:99795813..99800130,7	MCF-7	breast:

No data

Variant related genes	Relation type
MRPL30	TF binding region
C2orf15	TF binding region
MITD1	TF binding region
ENSG00000135951	Chromatin interaction
ENSG00000144182	Chromatin interaction
ENSG00000273155	Chromatin interaction
ENSG00000158411	Chromatin interaction
ENSG00000273045	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10865030	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12328219	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13384665	1.00[CEU][hapmap]
rs13393060	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13430662	0.92[EUR][1000 genomes]
rs4850896	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4851189	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4851191	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6542871	1.00[ASN][1000 genomes]
rs6728723	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7579999	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7586635	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs896884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

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	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1013507	chr2:99729047-99861692	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv961842	chr2:99781138-99886836	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99772400-99796400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:99772400-99796600	Weak transcription	Right Ventricle	heart
3	chr2:99772400-99796800	Weak transcription	Colonic Mucosa	Colon
4	chr2:99772400-99797000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:99772600-99796600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:99772600-99796600	Weak transcription	Fetal Kidney	kidney
7	chr2:99772600-99797000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr2:99772800-99796400	Weak transcription	Fetal Heart	heart
9	chr2:99773000-99796400	Weak transcription	Fetal Brain Male	brain
10	chr2:99774000-99796200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr2:99784600-99797000	Weak transcription	Ovary	ovary
12	chr2:99785200-99796000	Weak transcription	Spleen	Spleen
13	chr2:99785200-99796400	Weak transcription	NHEK	skin
14	chr2:99785200-99796600	Weak transcription	HSMMtube	muscle
15	chr2:99785200-99797000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:99786000-99796000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr2:99786600-99796600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr2:99786600-99797000	Weak transcription	Aorta	Aorta
19	chr2:99786600-99797000	Weak transcription	Esophagus	oesophagus
20	chr2:99786600-99797000	Weak transcription	Lung	lung
21	chr2:99787600-99796400	Weak transcription	HMEC	breast
22	chr2:99787600-99797000	Weak transcription	Psoas Muscle	Psoas
23	chr2:99787800-99796400	Weak transcription	NHLF	lung
24	chr2:99787800-99796600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr2:99789600-99796400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr2:99790000-99796400	Weak transcription	HSMM	muscle
27	chr2:99790200-99796400	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr2:99790400-99796200	Weak transcription	Fetal Muscle Trunk	muscle
29	chr2:99790400-99796400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr2:99790400-99796400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr2:99790400-99796400	Weak transcription	Fetal Intestine Small	intestine
32	chr2:99790600-99796400	Weak transcription	NHDF-Ad	bronchial
33	chr2:99790800-99796400	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr2:99790800-99796600	Weak transcription	Fetal Intestine Large	intestine
35	chr2:99792600-99797000	Weak transcription	Right Atrium	heart
36	chr2:99793600-99796400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr2:99794400-99796000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
38	chr2:99794600-99796200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:99794600-99796400	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr2:99794600-99796800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr2:99794800-99796600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr2:99794800-99796600	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr2:99794800-99796800	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr2:99795000-99796400	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr2:99795000-99796600	Enhancers	Monocytes-CD14+_RO01746	blood
46	chr2:99795000-99797000	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr2:99795200-99796400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr2:99795200-99796400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr2:99795200-99796600	Enhancers	Brain Angular Gyrus	brain
50	chr2:99795200-99796800	Enhancers	Skeletal Muscle Female	skeletal muscle

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