Variant report

Variant	rs3762984
Chromosome Location	chr5:95770307-95770308
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	REST	chr5:95769471-95770515	Hela-S3	cervix:	n/a	chr5:95770015-95770035 chr5:95770015-95770035 chr5:95770015-95770029 chr5:95770031-95770040
2	NFIC	chr5:95769770-95770460	ECC-1	luminal epithelium:	n/a	chr5:95770241-95770258 chr5:95770242-95770258
3	REST	chr5:95769611-95770427	MCF-7	breast:	n/a	chr5:95770015-95770035 chr5:95770015-95770035 chr5:95770015-95770029 chr5:95770031-95770040
4	TEAD4	chr5:95769681-95770318	A549	lung:	n/a	n/a
5	POU5F1	chr5:95769933-95770316	H1-hESC	embryonic stem cell:	n/a	n/a
6	REST	chr5:95769609-95770425	HCT-116	colon:	n/a	chr5:95770015-95770035 chr5:95770015-95770035 chr5:95770015-95770029 chr5:95770031-95770040
7	TCF7L2	chr5:95769943-95770339	Hela-S3	cervix:	n/a	n/a
8	CTCF	chr5:95770160-95770310	AG10803	skin:	n/a	n/a
9	REST	chr5:95769372-95770612	A549	lung:	n/a	chr5:95770015-95770035 chr5:95770015-95770035 chr5:95770015-95770029 chr5:95770031-95770040
10	MAX	chr5:95769904-95770362	Hela-S3	cervix:	n/a	n/a
11	REST	chr5:95769564-95770465	HCT-116	colon:	n/a	chr5:95770015-95770035 chr5:95770015-95770035 chr5:95770015-95770029 chr5:95770031-95770040
12	REST	chr5:95769493-95770646	PFSK-1	brain:	n/a	chr5:95770015-95770035 chr5:95770015-95770035 chr5:95770015-95770029 chr5:95770031-95770040
13	SIN3A	chr5:95769815-95770351	H1-hESC	embryonic stem cell:	n/a	chr5:95769817-95769826 chr5:95770016-95770030
14	REST	chr5:95769371-95770605	ECC-1	luminal epithelium:	n/a	chr5:95770015-95770035 chr5:95770015-95770035 chr5:95770015-95770029 chr5:95770031-95770040
15	SMC3	chr5:95769863-95770392	Hela-S3	cervix:	n/a	chr5:95770353-95770367
16	REST	chr5:95769523-95770457	PFSK-1	brain:	n/a	chr5:95770015-95770035 chr5:95770015-95770035 chr5:95770015-95770029 chr5:95770031-95770040
17	CTCF	chr5:95770180-95770330	MCF-7	breast:	n/a	n/a
18	REST	chr5:95769521-95770438	PANC-1	pancreas:	n/a	chr5:95770015-95770035 chr5:95770015-95770035 chr5:95770015-95770029 chr5:95770031-95770040
19	MYC	chr5:95770092-95770321	MCF10A-Er-Src	breast:	n/a	n/a
20	REST	chr5:95769549-95770484	SK-N-SH	brain:	n/a	chr5:95770015-95770035 chr5:95770015-95770035 chr5:95770015-95770029 chr5:95770031-95770040
21	REST	chr5:95769688-95770361	U87	brain:	n/a	chr5:95770015-95770035 chr5:95770015-95770035 chr5:95770015-95770029 chr5:95770031-95770040
22	REST	chr5:95769634-95770345	PFSK-1	brain:	n/a	chr5:95770015-95770035 chr5:95770015-95770035 chr5:95770015-95770029 chr5:95770031-95770040
23	REST	chr5:95769753-95770346	SK-N-SH	brain:	n/a	chr5:95770015-95770035 chr5:95770015-95770035 chr5:95770015-95770029 chr5:95770031-95770040
24	REST	chr5:95769510-95770573	MCF-7	breast:	n/a	chr5:95770015-95770035 chr5:95770015-95770035 chr5:95770015-95770029 chr5:95770031-95770040
25	REST	chr5:95766595-95770523	H1-neurons	neurons:	n/a	chr5:95770015-95770035 chr5:95770015-95770035 chr5:95768439-95768447 chr5:95770015-95770029 chr5:95770031-95770040
26	REST	chr5:95769749-95770350	HL-60	blood:	n/a	chr5:95770015-95770035 chr5:95770015-95770035 chr5:95770015-95770029 chr5:95770031-95770040
27	REST	chr5:95769690-95770359	U87	brain:	n/a	chr5:95770015-95770035 chr5:95770015-95770035 chr5:95770015-95770029 chr5:95770031-95770040
28	REST	chr5:95769629-95770388	A549	lung:	n/a	chr5:95770015-95770035 chr5:95770015-95770035 chr5:95770015-95770029 chr5:95770031-95770040
29	REST	chr5:95769673-95770350	Hela-S3	cervix:	n/a	chr5:95770015-95770035 chr5:95770015-95770035 chr5:95770015-95770029 chr5:95770031-95770040
30	REST	chr5:95769526-95770408	K562	blood:	n/a	chr5:95770015-95770035 chr5:95770015-95770035 chr5:95770015-95770029 chr5:95770031-95770040
31	RAD21	chr5:95769941-95770341	A549	lung:	n/a	chr5:95770180-95770190 chr5:95770180-95770192
32	RAD21	chr5:95769910-95770387	H1-hESC	embryonic stem cell:	n/a	chr5:95770180-95770190 chr5:95770180-95770192
33	TCF12	chr5:95769869-95770344	H1-hESC	embryonic stem cell:	n/a	chr5:95770103-95770110
34	POU5F1	chr5:95769801-95770438	H1-hESC	embryonic stem cell:	n/a	n/a
35	REST	chr5:95769289-95770532	HL-60	blood:	n/a	chr5:95770015-95770035 chr5:95770015-95770035 chr5:95770015-95770029 chr5:95770031-95770040
36	NFIC	chr5:95769831-95770485	SK-N-SH	brain:	n/a	chr5:95770241-95770258 chr5:95770242-95770258
37	REST	chr5:95769590-95770377	H1-hESC	embryonic stem cell:	n/a	chr5:95770015-95770035 chr5:95770015-95770035 chr5:95770015-95770029 chr5:95770031-95770040
38	ZNF143	chr5:95769842-95770377	H1-hESC	embryonic stem cell:	n/a	n/a
39	RAD21	chr5:95769899-95770386	Hela-S3	cervix:	n/a	chr5:95770180-95770190 chr5:95770180-95770192
40	EP300	chr5:95769988-95770316	SK-N-SH_RA	brain:	n/a	n/a
41	TFAP2C	chr5:95769818-95770473	Hela-S3	cervix:	n/a	n/a
42	MXI1	chr5:95769633-95770348	IMR90	lung:	n/a	n/a
43	REST	chr5:95769407-95770591	ECC-1	luminal epithelium:	n/a	chr5:95770015-95770035 chr5:95770015-95770035 chr5:95770015-95770029 chr5:95770031-95770040
44	REST	chr5:95769697-95770361	PANC-1	pancreas:	n/a	chr5:95770015-95770035 chr5:95770015-95770035 chr5:95770015-95770029 chr5:95770031-95770040
45	REST	chr5:95769439-95770609	PANC-1	pancreas:	n/a	chr5:95770015-95770035 chr5:95770015-95770035 chr5:95770015-95770029 chr5:95770031-95770040
46	NANOG	chr5:95769953-95770308	H1-hESC	embryonic stem cell:	n/a	n/a
47	JUND	chr5:95769861-95770378	H1-hESC	embryonic stem cell:	n/a	n/a
48	REST	chr5:95769561-95770354	HepG2	liver:	n/a	chr5:95770015-95770035 chr5:95770015-95770035 chr5:95770015-95770029 chr5:95770031-95770040
49	HDAC2	chr5:95769984-95770318	H1-hESC	embryonic stem cell:	n/a	n/a
50	ZNF143	chr5:95769880-95770392	Hela-S3	cervix:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CAST-9	chr5:95768987-95770845	NONHSAT102891

Variant related genes	Relation type
PCSK1	TF binding region

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs3792747	1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4869134	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030444	chr5:95353620-95995619	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv537810	chr5:95353620-95995619	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1024964	chr5:95742124-96065492	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv537811	chr5:95742124-96065492	Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv1026484	chr5:95759910-95961518	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95765000-95770400	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr5:95769200-95770400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr5:95769200-95770400	Bivalent Enhancer	Fetal Brain Male	brain
4	chr5:95769200-95770600	Bivalent Enhancer	NH-A	brain
5	chr5:95769400-95770400	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr5:95769400-95770400	Enhancers	Liver	Liver
7	chr5:95769400-95770400	Flanking Active TSS	Brain Angular Gyrus	brain
8	chr5:95769400-95770800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr5:95769400-95771000	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr5:95769600-95770400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
11	chr5:95769600-95770400	Enhancers	Adipose Nuclei	Adipose
12	chr5:95769600-95770400	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
13	chr5:95769600-95770600	Active TSS	Brain Germinal Matrix	brain
14	chr5:95769600-95770800	Enhancers	Right Atrium	heart
15	chr5:95769800-95770400	Bivalent Enhancer	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr5:95769800-95770400	Enhancers	Aorta	Aorta
17	chr5:95769800-95770400	Flanking Active TSS	Brain Hippocampus Middle	brain
18	chr5:95769800-95770400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr5:95769800-95770400	Bivalent Enhancer	Left Ventricle	heart
20	chr5:95769800-95770400	Enhancers	Pancreas	Pancrea
21	chr5:95769800-95770400	Enhancers	Hela-S3	cervix
22	chr5:95769800-95770600	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr5:95769800-95770800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr5:95769800-95770800	Enhancers	Psoas Muscle	Psoas
25	chr5:95770000-95770400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
26	chr5:95770000-95770400	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr5:95770000-95770400	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
28	chr5:95770000-95770400	Flanking Bivalent TSS/Enh	Brain Substantia Nigra	brain
29	chr5:95770000-95770400	Enhancers	Placenta	Placenta
30	chr5:95770000-95770400	Bivalent Enhancer	Lung	lung
31	chr5:95770000-95770400	Bivalent Enhancer	Osteobl	bone
32	chr5:95770000-95770600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr5:95770200-95770400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
34	chr5:95770200-95770400	Flanking Bivalent TSS/Enh	H9 Cell Line	embryonic stem cell
35	chr5:95770200-95770400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr5:95770200-95770400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
37	chr5:95770200-95770400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
38	chr5:95770200-95770400	Active TSS	Brain Anterior Caudate	brain
39	chr5:95770200-95770400	Enhancers	Brain Cingulate Gyrus	brain
40	chr5:95770200-95770400	Active TSS	Brain Inferior Temporal Lobe	brain
41	chr5:95770200-95770400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr5:95770200-95770400	Bivalent Enhancer	Fetal Brain Female	brain
43	chr5:95770200-95770400	Flanking Bivalent TSS/Enh	A549	lung
44	chr5:95770200-95770400	Flanking Active TSS	HUVEC	blood vessel
45	chr5:95770200-95770400	Bivalent Enhancer	NHEK	skin
46	chr5:95770200-95770600	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
47	chr5:95770200-95770600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
48	chr5:95770200-95770600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links