Variant report

Variant	rs56344180
Chromosome Location	chr2:37875681-37875682
allele	C/T
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	chr2:37867842-37879116	U87	brain:	n/a	n/a
2	REST	chr2:37875565-37875876	GM12878	blood:	n/a	chr2:37875788-37875801 chr2:37875785-37875805 chr2:37875785-37875805
3	POLR2A	chr2:37873373-37876259	SK-N-SH	brain:	n/a	n/a
4	REST	chr2:37875530-37875745	H1-hESC	embryonic stem cell:	n/a	n/a
5	WRNIP1	chr2:37875494-37875895	GM12878	blood:	n/a	n/a
6	REST	chr2:37875502-37875739	SK-N-SH	brain:	n/a	n/a
7	EP300	chr2:37875426-37875773	SK-N-SH_RA	brain:	n/a	n/a
8	POLR2A	chr2:37874506-37876510	GM12892	blood:	n/a	n/a
9	REST	chr2:37875562-37875895	HL-60	blood:	n/a	chr2:37875788-37875801 chr2:37875785-37875805 chr2:37875785-37875805
10	MAX	chr2:37875523-37876145	NB4	blood:	n/a	n/a
11	REST	chr2:37875351-37876067	HL-60	blood:	n/a	chr2:37875788-37875801 chr2:37875785-37875805 chr2:37875785-37875805
12	POLR2A	chr2:37874573-37876335	GM12878	blood:	n/a	n/a
13	REST	chr2:37875584-37875722	GM12878	blood:	n/a	n/a
14	REST	chr2:37875566-37875717	GM12878	blood:	n/a	n/a
15	POLR2A	chr2:37875539-37875837	GM12878	blood:	n/a	n/a
16	REST	chr2:37875497-37875766	PFSK-1	brain:	n/a	n/a
17	POLR2A	chr2:37874533-37876327	GM12878	blood:	n/a	n/a
18	NFATC1	chr2:37875186-37876155	GM12878	blood:	n/a	chr2:37875358-37875372
19	PML	chr2:37875390-37876291	GM12878	blood:	n/a	n/a
20	MTA3	chr2:37875514-37876158	GM12878	blood:	n/a	n/a
21	POLR2A	chr2:37875450-37876351	GM12892	blood:	n/a	n/a
22	CTCF	chr2:37875660-37875810	GM12872	blood:	n/a	n/a
23	POLR2A	chr2:37875491-37876023	K562	blood:	n/a	n/a
24	JUN	chr2:37875677-37876135	HUVEC	blood vessel:	n/a	n/a
25	POLR2A	chr2:37875556-37876137	HUVEC	blood vessel:	n/a	n/a
26	REST	chr2:37875470-37875778	ECC-1	luminal epithelium:	n/a	n/a
27	REST	chr2:37875431-37875936	PFSK-1	brain:	n/a	chr2:37875788-37875801 chr2:37875785-37875805 chr2:37875785-37875805
28	RUNX3	chr2:37875606-37876292	GM12878	blood:	n/a	n/a
29	REST	chr2:37875537-37875795	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr2:37875576-37876174	HUVEC	blood vessel:	n/a	n/a
31	POLR2A	chr2:37875665-37876245	U87	brain:	n/a	n/a
32	POLR2A	chr2:37874389-37877120	GM12891	blood:	n/a	n/a
33	POLR2A	chr2:37874623-37876203	GM19193	blood:	n/a	n/a
34	REST	chr2:37875517-37875794	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr2:37875254-37876344	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr2:37874489-37876313	GM12891	blood:	n/a	n/a
37	POLR2A	chr2:37871281-37876143	GM12878	blood:	n/a	n/a
38	REST	chr2:37875576-37875788	PFSK-1	brain:	n/a	n/a
39	POLR2A	chr2:37874425-37878298	GM12891	blood:	n/a	n/a
40	POLR2A	chr2:37872360-37878906	U87	brain:	n/a	n/a
41	POLR2A	chr2:37874392-37876318	GM12892	blood:	n/a	n/a
42	FOS	chr2:37875522-37876191	HUVEC	blood vessel:	n/a	n/a
43	POLR2A	chr2:37874398-37876426	GM12892	blood:	n/a	n/a
44	POLR2A	chr2:37874456-37876500	GM12891	blood:	n/a	n/a
45	REST	chr2:37875446-37875807	SK-N-SH	brain:	n/a	chr2:37875788-37875801 chr2:37875785-37875805 chr2:37875785-37875805
46	POLR2A	chr2:37875604-37875948	GM12891	blood:	n/a	n/a
47	REST	chr2:37875435-37875842	PFSK-1	brain:	n/a	chr2:37875788-37875801 chr2:37875785-37875805 chr2:37875785-37875805
48	POU2F2	chr2:37875240-37876116	GM12891	blood:	n/a	n/a

Variant related genes	Relation type
CDC42EP3	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12469780	0.87[ASN][1000 genomes]
rs12474331	0.86[ASN][1000 genomes]
rs4670746	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757793	chr2:37796654-38138939	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription 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	14 gene(s)	inside rSNPs	diseases
2	esv2759043	chr2:37796654-38138939	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv833825	chr2:37808169-37985917	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv535645	chr2:37853282-37972640	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv535646	chr2:37853282-38014428	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv873880	chr2:37868214-37926046	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv535647	chr2:37874563-38014428	Enhancers Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:37853600-37897400	Weak transcription	Small Intestine	intestine
2	chr2:37860800-37879600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:37864200-37880200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:37864400-37879400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr2:37866800-37881000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr2:37867000-37880600	Genic enhancers	Muscle Satellite Cultured Cells	--
7	chr2:37868000-37876200	Genic enhancers	Osteobl	bone
8	chr2:37868200-37876200	Genic enhancers	NH-A	brain
9	chr2:37868600-37879800	Genic enhancers	Primary monocytes fromperipheralblood	blood
10	chr2:37869400-37876200	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr2:37870800-37878600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:37871200-37875800	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr2:37871400-37880600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr2:37872000-37892400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr2:37872200-37881800	Weak transcription	Fetal Kidney	kidney
16	chr2:37872400-37880800	Weak transcription	Fetal Brain Male	brain
17	chr2:37873000-37881400	Enhancers	Right Atrium	heart
18	chr2:37873200-37876200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr2:37873200-37877200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:37873400-37876200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:37873400-37876800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr2:37873600-37876800	Weak transcription	Pancreas	Pancrea
23	chr2:37873600-37879600	Weak transcription	Gastric	stomach
24	chr2:37873600-37879600	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr2:37873600-37880200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr2:37873600-37881000	Weak transcription	Ovary	ovary
27	chr2:37873800-37889000	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr2:37874000-37876000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr2:37874000-37876200	ZNF genes & repeats	GM12878-XiMat	blood
30	chr2:37874200-37875800	Enhancers	Brain Hippocampus Middle	brain
31	chr2:37874200-37881600	Genic enhancers	NHLF	lung
32	chr2:37874400-37875800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:37874400-37881600	Enhancers	Psoas Muscle	Psoas
34	chr2:37874400-37883200	Enhancers	Adipose Nuclei	Adipose
35	chr2:37874600-37876000	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
36	chr2:37874600-37876000	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr2:37874600-37884000	Enhancers	Fetal Muscle Leg	muscle
38	chr2:37874600-37893000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:37874800-37875800	ZNF genes & repeats	Brain Germinal Matrix	brain
40	chr2:37874800-37875800	ZNF genes & repeats	Fetal Intestine Small	intestine
41	chr2:37874800-37876000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr2:37874800-37876200	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:37874800-37876200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr2:37874800-37876200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
45	chr2:37874800-37876200	Genic enhancers	Rectal Smooth Muscle	rectum
46	chr2:37874800-37876200	Genic enhancers	Thymus	Thymus
47	chr2:37874800-37876800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
48	chr2:37874800-37880000	Genic enhancers	Lung	lung
49	chr2:37874800-37882000	Enhancers	Left Ventricle	heart
50	chr2:37875000-37875800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links