Variant report

Variant	rs1723493
Chromosome Location	chr2:47385844-47385845
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:38)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:38 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:47382524-47406811	PFSK-1	brain:	n/a	n/a
2	POLR2A	chr2:47385615-47387337	K562	blood:	n/a	n/a
3	POLR2A	chr2:47385340-47386358	HepG2	liver:	n/a	n/a
4	POLR2A	chr2:47382225-47405286	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr2:47385491-47387192	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr2:47382104-47386243	MCF-7	breast:	n/a	n/a
7	POLR2A	chr2:47385326-47386375	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr2:47385320-47386260	GM12891	blood:	n/a	n/a
9	POLR2A	chr2:47385318-47387857	HepG2	liver:	n/a	n/a
10	POLR2A	chr2:47382411-47391126	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr2:47385462-47386324	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr2:47385585-47386409	A549	lung:	n/a	n/a
13	POLR2A	chr2:47385314-47385980	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr2:47382450-47387588	PANC-1	pancreas:	n/a	n/a
15	POLR2A	chr2:47382595-47387178	PANC-1	pancreas:	n/a	n/a
16	POLR2A	chr2:47385461-47386139	HUVEC	blood vessel:	n/a	n/a
17	POLR2A	chr2:47385327-47386386	GM12892	blood:	n/a	n/a
18	POLR2A	chr2:47385530-47387721	HepG2	liver:	n/a	n/a
19	POLR2A	chr2:47385235-47386294	GM12878	blood:	n/a	n/a
20	POLR2A	chr2:47382208-47387634	U87	brain:	n/a	n/a
21	BCL3	chr2:47385342-47386980	A549	lung:	n/a	n/a
22	POLR2A	chr2:47384626-47386313	HepG2	liver:	n/a	n/a
23	POLR2A	chr2:47385388-47387077	U87	brain:	n/a	n/a
24	POLR2A	chr2:47385232-47386330	K562	blood:	n/a	n/a
25	POLR2A	chr2:47385477-47387176	GM12891	blood:	n/a	n/a
26	NFATC1	chr2:47385520-47386190	GM12878	blood:	n/a	chr2:47385702-47385716
27	POLR2A	chr2:47382271-47387210	U87	brain:	n/a	n/a
28	POLR2A	chr2:47385392-47387077	U87	brain:	n/a	n/a
29	POLR2A	chr2:47385044-47386328	GM12892	blood:	n/a	n/a
30	POLR2A	chr2:47385383-47386475	GM12892	blood:	n/a	n/a
31	POLR2A	chr2:47385474-47386282	HUVEC	blood vessel:	n/a	n/a
32	POLR2A	chr2:47383059-47391091	K562	blood:	n/a	n/a
33	POLR2A	chr2:47385691-47386290	HCT-116	colon:	n/a	n/a
34	POLR2A	chr2:47385209-47386155	SK-N-MC	brain:	n/a	n/a
35	POLR2A	chr2:47385393-47386246	GM12891	blood:	n/a	n/a
36	POLR2A	chr2:47385842-47385847	HUVEC	blood vessel:	n/a	n/a
37	POLR2A	chr2:47385672-47386393	GM12892	blood:	n/a	n/a
38	POLR2A	chr2:47385518-47386431	GM12878	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:47384081..47386449-chr2:47504881..47507810,2	K562	blood:
2	chr2:47383453..47385887-chr2:47388520..47390045,2	MCF-7	breast:
3	chr2:47385656..47388232-chr2:47538182..47540860,2	MCF-7	breast:

No data

Variant related genes	Relation type
C2orf61	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11685529	1.00[CHB][hapmap]
rs13430277	0.81[CEU][hapmap]
rs1353644	0.95[ASN][1000 genomes]
rs1693869	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1693890	0.81[ASN][1000 genomes]
rs1723482	0.86[CEU][hapmap];0.82[JPT][hapmap]
rs1723483	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1723484	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs1723486	0.81[ASN][1000 genomes]
rs2454081	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs815802	0.86[ASW][hapmap];0.82[JPT][hapmap];0.81[LWK][hapmap];0.80[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs815807	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs815808	0.81[CHD][hapmap]
rs815811	0.93[ASN][1000 genomes]
rs815815	1.00[CEU][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs815816	0.92[CEU][hapmap];0.93[MEX][hapmap];0.84[AMR][1000 genomes];0.82[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	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
3	nsv457374	chr2:47313624-47448865	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
4	nsv581754	chr2:47313624-47448865	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1723493	CALM2	cis	cerebellum	SCAN
rs1723493	STON1-GTF2A1L	cis	cerebellum	SCAN
rs1723493	TTC7A	cis	cerebellum	SCAN
rs1723493	CALM2	cis	parietal	SCAN
rs1723493	C2orf61	cis	cerebellum	SCAN
rs1723493	ABCG8	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47357000-47386600	Weak transcription	Fetal Heart	heart
2	chr2:47357000-47386800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:47357200-47386400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr2:47360600-47386800	Weak transcription	Stomach Mucosa	stomach
5	chr2:47363400-47386400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr2:47366200-47397000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:47366800-47399400	Strong transcription	Fetal Thymus	thymus
8	chr2:47367000-47401200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr2:47367200-47402000	Weak transcription	Esophagus	oesophagus
10	chr2:47367600-47386800	Weak transcription	Right Ventricle	heart
11	chr2:47367600-47387400	Weak transcription	Pancreas	Pancrea
12	chr2:47369200-47386800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:47369600-47386200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr2:47369800-47386800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr2:47369800-47386800	Weak transcription	Psoas Muscle	Psoas
16	chr2:47369800-47391200	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr2:47370000-47389600	Strong transcription	Muscle Satellite Cultured Cells	--
18	chr2:47371200-47388200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr2:47371400-47386600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr2:47371600-47389800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:47371800-47392200	Strong transcription	Osteobl	bone
22	chr2:47372000-47386800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr2:47372600-47386800	Weak transcription	Gastric	stomach
24	chr2:47372600-47396800	Weak transcription	Small Intestine	intestine
25	chr2:47375400-47386000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr2:47375600-47397400	Weak transcription	Fetal Brain Male	brain
27	chr2:47376000-47388000	Strong transcription	HSMM	muscle
28	chr2:47376400-47389800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:47377400-47386400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr2:47377400-47386800	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr2:47377600-47386600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr2:47377600-47386800	Weak transcription	Colonic Mucosa	Colon
33	chr2:47378200-47386800	Weak transcription	K562	blood
34	chr2:47378400-47392000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr2:47378600-47386000	Weak transcription	Brain Substantia Nigra	brain
36	chr2:47378600-47386800	Weak transcription	Brain Angular Gyrus	brain
37	chr2:47378600-47386800	Weak transcription	Ovary	ovary
38	chr2:47378600-47388000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr2:47378600-47389800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr2:47379000-47386800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr2:47380200-47391400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr2:47380600-47388000	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr2:47381400-47389600	Strong transcription	Fetal Brain Female	brain
44	chr2:47381600-47390400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr2:47382000-47391000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr2:47382200-47390000	Strong transcription	NHLF	lung
47	chr2:47382600-47386000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr2:47382600-47386400	Weak transcription	Brain Germinal Matrix	brain
49	chr2:47382600-47391400	Strong transcription	NH-A	brain
50	chr2:47382600-47398200	Weak transcription	Aorta	Aorta

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