Variant report

Variant	rs55813407
Chromosome Location	chr2:47260829-47260830
allele	C/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	chr2:47260197-47262901	HepG2	liver:	n/a	n/a
2	MAFK	chr2:47260769-47262230	HepG2	liver:	n/a	n/a
3	ZBTB7A	chr2:47260820-47262208	ECC-1	luminal epithelium:	n/a	n/a
4	MXI1	chr2:47258782-47264116	SK-N-SH	brain:	n/a	chr2:47261692-47261707
5	RAD21	chr2:47258361-47262673	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr2:47260357-47261992	SK-N-SH	brain:	n/a	n/a
7	SP1	chr2:47260506-47262645	A549	lung:	n/a	chr2:47261845-47261859
8	MAX	chr2:47260731-47263085	A549	lung:	n/a	chr2:47262041-47262050 chr2:47262040-47262051 chr2:47262040-47262051 chr2:47262039-47262052
9	MBD4	chr2:47260498-47263693	HepG2	liver:	n/a	n/a
10	POLR2A	chr2:47260246-47262724	HepG2	liver:	n/a	n/a
11	SP1	chr2:47260598-47262689	A549	lung:	n/a	chr2:47261845-47261859
12	SMC3	chr2:47258831-47263561	SK-N-SH	brain:	n/a	chr2:47259083-47259093
13	POLR2A	chr2:47259936-47262330	IMR90	lung:	n/a	n/a
14	MYBL2	chr2:47260042-47260830	HepG2	liver:	n/a	n/a
15	SIN3A	chr2:47260824-47260996	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr2:47260620-47262254	Hela-S3	cervix:	n/a	n/a
17	NFIC	chr2:47260809-47262129	SK-N-SH	brain:	n/a	n/a
18	BHLHE40	chr2:47260184-47262789	HepG2	liver:	n/a	chr2:47262041-47262050 chr2:47262042-47262051 chr2:47262041-47262050
19	BCL3	chr2:47260131-47262418	A549	lung:	n/a	chr2:47261600-47261607
20	POLR2A	chr2:47260556-47262072	HepG2	liver:	n/a	n/a
21	MAZ	chr2:47260037-47262281	IMR90	lung:	n/a	chr2:47262041-47262050 chr2:47262040-47262051 chr2:47262040-47262051 chr2:47262039-47262052
22	CTCF	chr2:47260088-47262012	SK-N-SH	brain:	n/a	n/a
23	TCF12	chr2:47260461-47263474	A549	lung:	n/a	chr2:47263338-47263345
24	RCOR1	chr2:47260043-47262802	IMR90	lung:	n/a	n/a
25	POLR2A	chr2:47260637-47263389	HepG2	liver:	n/a	n/a
26	MXI1	chr2:47260131-47262696	HepG2	liver:	n/a	chr2:47261692-47261707
27	MAZ	chr2:47260696-47262411	HepG2	liver:	n/a	chr2:47262041-47262050 chr2:47262040-47262051 chr2:47262040-47262051 chr2:47262039-47262052
28	FOSL2	chr2:47260251-47262228	A549	lung:	n/a	n/a
29	TFAP2C	chr2:47260284-47261960	Hela-S3	cervix:	n/a	n/a
30	MAX	chr2:47260279-47262986	HepG2	liver:	n/a	chr2:47262041-47262050 chr2:47262040-47262051 chr2:47262040-47262051 chr2:47262039-47262052
31	CTCF	chr2:47260007-47262867	A549	lung:	n/a	n/a
32	POLR2A	chr2:47260568-47260998	HepG2	liver:	n/a	n/a
33	POLR2A	chr2:47260395-47262146	Hela-S3	cervix:	n/a	n/a
34	CHD2	chr2:47260789-47260986	HepG2	liver:	n/a	n/a
35	SIX5	chr2:47260505-47262038	A549	lung:	n/a	n/a
36	BRCA1	chr2:47260648-47262049	HepG2	liver:	n/a	n/a
37	PBX3	chr2:47260493-47262185	SK-N-SH	brain:	n/a	n/a
38	REST	chr2:47260593-47262078	A549	lung:	n/a	n/a
39	MAX	chr2:47260022-47263662	HepG2	liver:	n/a	chr2:47262041-47262050 chr2:47262040-47262051 chr2:47262040-47262051 chr2:47262039-47262052
40	HEY1	chr2:47260828-47262365	HepG2	liver:	n/a	chr2:47262041-47262050 chr2:47262154-47262163
41	POLR2A	chr2:47260525-47262407	H1-hESC	embryonic stem cell:	n/a	n/a
42	EP300	chr2:47260730-47262709	A549	lung:	n/a	n/a
43	POLR2A	chr2:47260230-47262056	HUVEC	blood vessel:	n/a	n/a
44	NFIC	chr2:47260632-47263635	HepG2	liver:	n/a	n/a
45	MXI1	chr2:47260047-47262776	IMR90	lung:	n/a	chr2:47261692-47261707
46	HDAC2	chr2:47260636-47262752	HepG2	liver:	n/a	chr2:47261239-47261253
47	TCF12	chr2:47260010-47262085	SK-N-SH	brain:	n/a	n/a
48	NFIC	chr2:47260675-47262419	SK-N-SH	brain:	n/a	n/a
49	PBX3	chr2:47260678-47262135	A549	lung:	n/a	n/a
50	POLR2A	chr2:47260417-47261681	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:47247505..47249498-chr2:47258978..47261043,2	K562	blood:
2	chr2:47260087..47265958-chr2:47400378..47404964,8	K562	blood:
3	chr2:47247292..47249498-chr2:47258978..47261257,2	K562	blood:
4	chr2:47252232..47263251-chr2:47397787..47406051,20	MCF-7	breast:

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

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12373629	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13398062	0.95[ASN][1000 genomes]
rs28490098	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55813111	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55829028	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55855730	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55920732	0.91[ASN][1000 genomes]
rs6729896	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72808511	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72808512	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72808515	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72808516	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72808520	0.91[ASN][1000 genomes]
rs7563297	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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
6	nsv1000377	chr2:47189386-47344029	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv525197	chr2:47210747-47297973	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv518312	chr2:47224927-47262137	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv984532	chr2:47237908-47270533	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv581752	chr2:47248111-47262137	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv457363	chr2:47249239-47263232	Transcr. at gene 5' and 3' Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv581753	chr2:47249239-47263232	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv528091	chr2:47249239-47273732	Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47214000-47262000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr2:47230200-47302800	Strong transcription	Dnd41	blood
3	chr2:47232000-47265000	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr2:47234400-47283600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr2:47236000-47278600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr2:47243800-47261000	Weak transcription	K562	blood
7	chr2:47244200-47261200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr2:47245800-47268600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr2:47246000-47261800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr2:47246000-47283800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr2:47246200-47261400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr2:47246800-47281600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr2:47247400-47263000	Strong transcription	Primary T helper cells PMA-I stimulated	--
14	chr2:47251600-47265000	Strong transcription	Primary T cells from cord blood	blood
15	chr2:47251600-47266000	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr2:47252000-47283400	Strong transcription	Thymus	Thymus
17	chr2:47253400-47261400	Strong transcription	GM12878-XiMat	blood
18	chr2:47253400-47263000	Genic enhancers	Esophagus	oesophagus
19	chr2:47255600-47261200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:47255600-47273400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr2:47256600-47261000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:47256800-47261000	Genic enhancers	HMEC	breast
23	chr2:47256800-47264000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:47257000-47261200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr2:47257000-47261200	Genic enhancers	NHLF	lung
26	chr2:47257000-47262200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr2:47257000-47277000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr2:47257200-47261200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr2:47257200-47261200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr2:47257400-47262800	Enhancers	Psoas Muscle	Psoas
31	chr2:47257600-47265200	Genic enhancers	Spleen	Spleen
32	chr2:47257600-47267800	Genic enhancers	Fetal Muscle Leg	muscle
33	chr2:47257800-47262800	Genic enhancers	Fetal Stomach	stomach
34	chr2:47258000-47261400	Weak transcription	Fetal Brain Female	brain
35	chr2:47258400-47268400	Genic enhancers	Fetal Thymus	thymus
36	chr2:47258400-47282600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr2:47258600-47263400	Enhancers	Liver	Liver
38	chr2:47258600-47263400	Enhancers	Placenta Amnion	Placenta Amnion
39	chr2:47258600-47265200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr2:47258800-47261000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr2:47258800-47261200	Genic enhancers	Primary monocytes fromperipheralblood	blood
42	chr2:47258800-47263200	Enhancers	HUVEC	blood vessel
43	chr2:47258800-47263400	Enhancers	Left Ventricle	heart
44	chr2:47259000-47261000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr2:47259000-47262400	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr2:47259000-47263000	Genic enhancers	Duodenum Mucosa	Duodenum
47	chr2:47259000-47263200	Genic enhancers	Rectal Mucosa Donor 29	rectum
48	chr2:47259000-47263200	Enhancers	Right Atrium	heart
49	chr2:47259000-47263200	Enhancers	NH-A	brain
50	chr2:47259000-47263800	Enhancers	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links