Variant report

Variant	rs2336546
Chromosome Location	chr3:52869769-52869770
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:52869738-52869788	PANC-1	pancreas:	n/a
2	chr3:52869738-52869788	AG04449	skin:	fetal
3	chr3:52869738-52869788	HepG2	liver:	n/a
4	chr3:52869738-52869788	HRE	kidney:	n/a
5	chr3:52869738-52869788	AoSMC	blood vessel:	n/a
6	chr3:52869738-52869788	NB4	blood:	n/a
7	chr3:52869738-52869788	A549	lung:	n/a
8	chr3:52869738-52869788	HIPEpiC	eye:	n/a
9	chr3:52869738-52869788	NHBE	bronchial:	n/a
10	chr3:52869738-52869788	HEK293	kidney:	embryo
11	chr3:52869738-52869788	AG04450	lung:	fetal
12	chr3:52869738-52869788	SKMC	muscle:	n/a
13	chr3:52869738-52869788	GM19239	blood:	n/a
14	chr3:52869738-52869788	GM12892	blood:	n/a
15	chr3:52869738-52869788	NH-A	brain:	n/a
16	chr3:52869738-52869788	NT2-D1	testis:	n/a
17	chr3:52869738-52869788	K562	blood:	n/a
18	chr3:52869738-52869788	HPAEpiC	pulmonary alveolar:	n/a
19	chr3:52869738-52869788	HRCEpiC	kidney:	n/a
20	chr3:52869738-52869788	SAEC	small airway:	n/a
21	chr3:52869738-52869788	MCF10A-Er-Src	breast:	n/a
22	chr3:52869738-52869788	HCT-116	colon:	n/a
23	chr3:52869738-52869788	HAEpiC	amniotic membrane:	n/a
24	chr3:52869738-52869788	Hepatocyte	liver:	n/a
25	chr3:52869738-52869788	IMR90	lung:	fetal
26	chr3:52869738-52869788	LNCaP	prostate:	n/a
27	chr3:52869738-52869788	AG09309	skin:	n/a
28	chr3:52869738-52869788	NHDF-neo	bronchial:	n/a
29	chr3:52869738-52869788	HRPEpiC	eye:	n/a
30	chr3:52869738-52869788	HEEpiC	esophagus:	n/a
31	chr3:52869738-52869788	GM12891	blood:	n/a
32	chr3:52869738-52869788	U87	brain:	n/a
33	chr3:52869738-52869788	ECC-1	luminal epithelium:	n/a
34	chr3:52869738-52869788	HL-60	blood:	n/a
35	chr3:52869738-52869788	MCF-7	breast:	n/a
36	chr3:52869738-52869788	HCM	heart:	n/a
37	chr3:52869738-52869788	Jurkat	blood:	n/a
38	chr3:52869738-52869788	BJ	skin:	n/a
39	chr3:52869738-52869788	H1-hESC	embryonic stem cell:	embryo
40	chr3:52869738-52869788	GM06990	blood:	n/a
41	chr3:52869738-52869788	CMK	blood:	n/a
42	chr3:52869738-52869788	SK-N-SH	brain:	n/a
43	chr3:52869738-52869788	PFSK-1	brain:	n/a
44	chr3:52869738-52869788	HNPCEpiC	eye:	n/a
45	chr3:52869738-52869788	SK-N-SH_RA	brain:	n/a
46	chr3:52869738-52869788	T-47D	breast:	n/a
47	chr3:52869738-52869788	Caco-2	colon:	n/a
48	chr3:52869738-52869788	RPTEC	kidney:	n/a
49	chr3:52869738-52869788	Hela-S3	cervix:	n/a
50	chr3:52869738-52869788	GM12878	blood:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52867798..52869834-chr3:52876401..52878497,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000243696	CpG island
MUSTN1	CpG island
ITIH4	CpG island
ENSG00000213533	Chromatin interaction
ENSG00000248592	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10049313	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1052728	0.91[AMR][1000 genomes]
rs13066997	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1986738	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1986739	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2001733	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2001734	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2245536	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2246888	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2246889	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2256728	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2256734	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2276814	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2276819	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2276821	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2336155	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2336157	0.91[AMR][1000 genomes]
rs2336158	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2336159	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2336556	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2336557	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2336559	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2535615	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2535616	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2535617	0.90[AFR][1000 genomes]
rs2535618	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2535619	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2535620	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2535621	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2535622	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2535623	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2535626	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2535628	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2535631	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2535632	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2535636	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2535637	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2535638	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2535639	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2535641	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2535642	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2535643	1.00[AMR][1000 genomes]
rs2535644	1.00[AMR][1000 genomes]
rs2535645	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2710318	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2710319	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2710320	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2710321	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2710324	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2710325	0.90[AFR][1000 genomes]
rs2710328	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2710343	0.91[AMR][1000 genomes]
rs2710344	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2878633	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2878634	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2878635	0.91[AMR][1000 genomes]
rs2878636	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3774361	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4234637	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4687555	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4687557	0.91[AMR][1000 genomes]
rs4687659	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4687661	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4687665	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4687666	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4687667	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4687668	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs4687669	0.91[AMR][1000 genomes]
rs4687670	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4687671	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4687674	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4687675	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6445540	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6445542	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs6774869	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6776990	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6791937	0.91[AMR][1000 genomes]
rs7623667	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7629528	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7637212	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7638431	0.92[AFR][1000 genomes]
rs7645169	0.93[AFR][1000 genomes]
rs7647534	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7649515	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7650966	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7652476	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9681089	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9682449	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs9682819	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9877711	0.91[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	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
2	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv876797	chr3:52817675-52873984	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52854200-52874200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:52854800-52888400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:52856000-52875000	Weak transcription	Fetal Intestine Large	intestine
4	chr3:52862000-52882600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:52863200-52872600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr3:52864400-52875800	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr3:52865600-52874200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:52865600-52875200	Weak transcription	Dnd41	blood
9	chr3:52865800-52878600	Weak transcription	Small Intestine	intestine
10	chr3:52866000-52869800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:52866000-52884800	Weak transcription	HMEC	breast
12	chr3:52866200-52870200	Weak transcription	Gastric	stomach
13	chr3:52866200-52872600	Weak transcription	Duodenum Mucosa	Duodenum
14	chr3:52866200-52872600	Weak transcription	Esophagus	oesophagus
15	chr3:52866200-52885200	Weak transcription	NHEK	skin
16	chr3:52866400-52869800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:52866400-52871800	Strong transcription	Primary T cells from cord blood	blood
18	chr3:52866400-52872400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:52866600-52869800	Enhancers	Liver	Liver
20	chr3:52866600-52869800	Weak transcription	Brain Hippocampus Middle	brain
21	chr3:52866600-52873600	Weak transcription	Hela-S3	cervix
22	chr3:52866600-52879200	Weak transcription	Osteobl	bone
23	chr3:52866800-52871000	Strong transcription	Spleen	Spleen
24	chr3:52866800-52872000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:52866800-52876400	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr3:52866800-52878200	Strong transcription	Fetal Brain Female	brain
27	chr3:52866800-52879600	Genic enhancers	Fetal Thymus	thymus
28	chr3:52867000-52870600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:52867000-52871000	Strong transcription	Thymus	Thymus
30	chr3:52867000-52871200	Weak transcription	Pancreas	Pancrea
31	chr3:52867000-52876400	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr3:52867000-52881600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr3:52867000-52881800	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr3:52867200-52871400	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr3:52867200-52875200	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr3:52867400-52870000	Flanking Active TSS	Fetal Muscle Trunk	muscle
37	chr3:52867600-52871800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr3:52867800-52870600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:52867800-52871200	Enhancers	Right Ventricle	heart
40	chr3:52868000-52878800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr3:52868000-52883200	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr3:52868200-52870000	Enhancers	Fetal Lung	lung
43	chr3:52868200-52870200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:52868400-52870200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr3:52868400-52870200	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr3:52868400-52871400	Enhancers	Fetal Heart	heart
47	chr3:52868400-52877800	Strong transcription	Brain Germinal Matrix	brain
48	chr3:52868600-52869800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr3:52868600-52870000	Weak transcription	Brain Cingulate Gyrus	brain
50	chr3:52868600-52870400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links