Variant report

Variant	rs56875665
Chromosome Location	chr2:47395765-47395766
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 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	chr2:47395765-47395866	K562	blood:	n/a	n/a
3	POLR2A	chr2:47382225-47405286	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr2:47394862-47395945	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr2:47395372-47395898	GM12892	blood:	n/a	n/a
6	POLR2A	chr2:47395032-47395845	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr2:47395605-47395823	ProgFib	skin:	n/a	n/a
8	POLR2A	chr2:47395156-47395842	U87	brain:	n/a	n/a
9	POLR2A	chr2:47395520-47395834	HepG2	liver:	n/a	n/a
10	POLR2A	chr2:47395660-47395935	K562	blood:	n/a	n/a
11	POLR2A	chr2:47395658-47395943	K562	blood:	n/a	n/a
12	POLR2A	chr2:47394900-47395915	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:47394184..47396929-chr2:47499010..47501713,3	MCF-7	breast:
2	chr2:47395420..47397137-chr2:47479319..47481186,2	K562	blood:
3	chr2:47229922..47232405-chr2:47395571..47398538,2	K562	blood:
4	chr2:47393811..47396441-chr2:47676637..47679621,2	K562	blood:
5	chr2:47140871..47143064-chr2:47395093..47397329,3	MCF-7	breast:
6	chr2:47395269..47398223-chr2:47446895..47449256,2	K562	blood:
7	chr2:47392985..47395807-chr2:47465874..47467889,2	K562	blood:

No data

Variant related genes	Relation type
CALM2	TF binding region
ENSG00000180398	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11842	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17036300	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17036311	0.94[AMR][1000 genomes]
rs17036313	0.80[AMR][1000 genomes]
rs17036316	0.94[AMR][1000 genomes]
rs17036320	0.98[AMR][1000 genomes]
rs17036325	0.98[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2016682	1.00[ASN][1000 genomes]
rs2347617	0.94[AMR][1000 genomes]
rs4953469	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4953470	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4953471	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4953472	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59415749	0.90[AMR][1000 genomes]
rs6713257	0.94[AMR][1000 genomes]
rs6719174	0.90[AFR][1000 genomes]
rs6749284	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6760339	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72810414	0.90[AMR][1000 genomes]
rs72810415	0.88[AMR][1000 genomes]
rs72810417	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72810419	0.98[AMR][1000 genomes]
rs72810439	0.82[AFR][1000 genomes]
rs72877054	0.88[AMR][1000 genomes]
rs7583684	0.81[AMR][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

No data

Chromatin state (count:127 , 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	chr2:47372600-47396800	Weak transcription	Small Intestine	intestine
6	chr2:47375600-47397400	Weak transcription	Fetal Brain Male	brain
7	chr2:47382600-47398200	Weak transcription	Aorta	Aorta
8	chr2:47384400-47397200	Weak transcription	Right Atrium	heart
9	chr2:47384800-47397600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr2:47385000-47398000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr2:47385400-47397800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:47385400-47397800	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr2:47385400-47398400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr2:47385400-47398600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:47385400-47398800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr2:47385600-47397200	Strong transcription	NHEK	skin
17	chr2:47385600-47397600	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr2:47385600-47398200	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr2:47385600-47398600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr2:47385800-47396400	Strong transcription	HMEC	breast
21	chr2:47386000-47398800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:47386600-47399000	Genic enhancers	HepG2	liver
23	chr2:47386800-47397800	Strong transcription	K562	blood
24	chr2:47387600-47401400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:47387600-47402200	Weak transcription	Gastric	stomach
26	chr2:47387800-47402000	Weak transcription	Pancreas	Pancrea
27	chr2:47388800-47397600	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr2:47389200-47396200	Weak transcription	Lung	lung
29	chr2:47389200-47397000	Weak transcription	Brain Germinal Matrix	brain
30	chr2:47389200-47402000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr2:47389400-47400200	Weak transcription	Colonic Mucosa	Colon
32	chr2:47389600-47396800	Weak transcription	Fetal Brain Female	brain
33	chr2:47389800-47396800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr2:47390000-47396800	Genic enhancers	NHLF	lung
35	chr2:47390000-47397200	Weak transcription	HSMMtube	muscle
36	chr2:47390000-47397400	Weak transcription	Psoas Muscle	Psoas
37	chr2:47390000-47402000	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr2:47390200-47399200	Weak transcription	Fetal Kidney	kidney
39	chr2:47390400-47396800	Genic enhancers	A549	lung
40	chr2:47390600-47397400	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr2:47391000-47396200	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr2:47391000-47396800	Genic enhancers	Brain Inferior Temporal Lobe	brain
43	chr2:47391000-47397000	Weak transcription	Fetal Lung	lung
44	chr2:47391000-47398800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr2:47391400-47397600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr2:47391600-47397200	Strong transcription	HUVEC	blood vessel
47	chr2:47391600-47397600	Strong transcription	Primary B cells from peripheral blood	blood
48	chr2:47391600-47398000	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr2:47391800-47397200	Genic enhancers	Brain Cingulate Gyrus	brain
50	chr2:47391800-47397200	Genic enhancers	NHDF-Ad	bronchial

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