Variant report

Variant	rs815802
Chromosome Location	chr2:47392049-47392050
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:29)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:29 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:47391717-47393295	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr2:47391883-47393687	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:47382524-47406811	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr2:47382225-47405286	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr2:47391972-47392533	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr2:47391381-47393627	U87	brain:	n/a	n/a
7	POLR2A	chr2:47391410-47394606	K562	blood:	n/a	n/a
8	POLR2A	chr2:47391459-47393002	A549	lung:	n/a	n/a
9	POLR2A	chr2:47391908-47392101	ProgFib	skin:	n/a	n/a
10	POLR2A	chr2:47391788-47392106	HepG2	liver:	n/a	n/a
11	POLR2A	chr2:47391797-47392088	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr2:47391861-47392094	K562	blood:	n/a	n/a
13	POLR2A	chr2:47391850-47393368	K562	blood:	n/a	n/a
14	POLR2A	chr2:47391986-47393031	GM12892	blood:	n/a	n/a
15	POLR2A	chr2:47391829-47392681	GM12878	blood:	n/a	n/a
16	POLR2A	chr2:47391730-47392545	U87	brain:	n/a	n/a
17	POLR2A	chr2:47391949-47392115	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr2:47391860-47392126	HepG2	liver:	n/a	n/a
19	POLR2A	chr2:47391730-47393750	U87	brain:	n/a	n/a
20	POLR2A	chr2:47391841-47392482	GM12892	blood:	n/a	n/a
21	POLR2A	chr2:47391920-47392568	GM12878	blood:	n/a	n/a
22	POLR2A	chr2:47391916-47392564	HepG2	liver:	n/a	n/a
23	POLR2A	chr2:47391508-47393234	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr2:47391952-47392129	HepG2	liver:	n/a	n/a
25	POLR2A	chr2:47391289-47392127	SK-N-MC	brain:	n/a	n/a
26	POLR2A	chr2:47391330-47393643	SK-N-SH	brain:	n/a	n/a
27	POLR2A	chr2:47392006-47393156	GM12891	blood:	n/a	n/a
28	POLR2A	chr2:47391378-47392082	MCF-7	breast:	n/a	n/a
29	POLR2A	chr2:47391363-47393627	U87	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:47214614..47216991-chr2:47391312..47393709,3	K562	blood:

No data

Variant related genes	Relation type
CALM2	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11125126	0.90[CHB][hapmap];0.90[CHD][hapmap];0.87[ASN][1000 genomes]
rs12991318	0.90[CHB][hapmap]
rs13430277	0.80[CHB][hapmap]
rs1404770	0.83[ASN][1000 genomes]
rs1630239	0.88[ASN][1000 genomes]
rs1693863	0.88[ASN][1000 genomes]
rs1693864	0.94[ASN][1000 genomes]
rs1693869	0.82[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs1693882	0.95[ASN][1000 genomes]
rs1693890	0.80[EUR][1000 genomes]
rs1723482	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1723483	0.82[AFR][1000 genomes]
rs1723484	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1723486	0.80[EUR][1000 genomes]
rs1723493	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]
rs1995108	0.86[ASN][1000 genomes]
rs2454082	0.98[ASN][1000 genomes]
rs2454083	0.98[ASN][1000 genomes]
rs2462588	0.86[ASN][1000 genomes]
rs2462589	0.86[ASN][1000 genomes]
rs6713934	0.88[ASN][1000 genomes]
rs6751198	0.87[ASN][1000 genomes]
rs72879030	0.81[ASN][1000 genomes]
rs7606478	0.88[ASN][1000 genomes]
rs815815	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs815816	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs815817	0.87[ASN][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs815802	CALM2	cis	parietal	SCAN
rs815802	C2orf61	cis	cerebellum	SCAN
rs815802	STON1-GTF2A1L	cis	cerebellum	SCAN
rs815802	CALM2	cis	cerebellum	SCAN
rs815802	TTC7A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47366200-47397000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr2:47366800-47399400	Strong transcription	Fetal Thymus	thymus
3	chr2:47367000-47401200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:47367200-47402000	Weak transcription	Esophagus	oesophagus
5	chr2:47371800-47392200	Strong transcription	Osteobl	bone
6	chr2:47372600-47396800	Weak transcription	Small Intestine	intestine
7	chr2:47375600-47397400	Weak transcription	Fetal Brain Male	brain
8	chr2:47382600-47398200	Weak transcription	Aorta	Aorta
9	chr2:47384400-47397200	Weak transcription	Right Atrium	heart
10	chr2:47384600-47393200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr2:47384800-47397600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:47385000-47392400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:47385000-47398000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:47385200-47392400	Strong transcription	Primary T cells from cord blood	blood
15	chr2:47385200-47392400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr2:47385200-47393200	Strong transcription	Fetal Muscle Leg	muscle
17	chr2:47385400-47392400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:47385400-47392600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr2:47385400-47392800	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr2:47385400-47392800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:47385400-47397800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:47385400-47397800	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr2:47385400-47398400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr2:47385400-47398600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr2:47385400-47398800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr2:47385600-47392400	Strong transcription	Dnd41	blood
27	chr2:47385600-47397200	Strong transcription	NHEK	skin
28	chr2:47385600-47397600	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr2:47385600-47398200	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr2:47385600-47398600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr2:47385800-47396400	Strong transcription	HMEC	breast
32	chr2:47386000-47398800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:47386400-47393200	Strong transcription	Primary hematopoietic stem cells	blood
34	chr2:47386600-47399000	Genic enhancers	HepG2	liver
35	chr2:47386800-47397800	Strong transcription	K562	blood
36	chr2:47387600-47401400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:47387600-47402200	Weak transcription	Gastric	stomach
38	chr2:47387800-47402000	Weak transcription	Pancreas	Pancrea
39	chr2:47388200-47393400	Strong transcription	Fetal Intestine Large	intestine
40	chr2:47388400-47393000	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr2:47388800-47397600	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr2:47389000-47392200	Weak transcription	Stomach Mucosa	stomach
43	chr2:47389200-47393200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr2:47389200-47396200	Weak transcription	Lung	lung
45	chr2:47389200-47397000	Weak transcription	Brain Germinal Matrix	brain
46	chr2:47389200-47402000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr2:47389400-47400200	Weak transcription	Colonic Mucosa	Colon
48	chr2:47389600-47396800	Weak transcription	Fetal Brain Female	brain
49	chr2:47389800-47393000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr2:47389800-47393600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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