Variant report

Variant	rs2240897
Chromosome Location	chr3:52526535-52526536
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:52526328-52526547	K562	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:52526520-52526570	GM12892	blood:	n/a
2	chr3:52526520-52526570	HEEpiC	esophagus:	n/a
3	chr3:52526520-52526570	HCM	heart:	n/a
4	chr3:52526520-52526570	NHBE	bronchial:	n/a
5	chr3:52526520-52526570	U87	brain:	n/a
6	chr3:52526520-52526570	HCPEpiC	choroid plexus:	n/a
7	chr3:52526520-52526570	GM06990	blood:	n/a
8	chr3:52526520-52526570	HMEC	breast:	n/a
9	chr3:52526520-52526570	A549	lung:	n/a
10	chr3:52526520-52526570	Hepatocyte	liver:	n/a
11	chr3:52526520-52526570	SK-N-MC	brain:	n/a
12	chr3:52526520-52526570	NH-A	brain:	n/a
13	chr3:52526520-52526570	HEK293	kidney:	embryo
14	chr3:52526520-52526570	GM12891	blood:	n/a
15	chr3:52526520-52526570	MCF-7	breast:	n/a
16	chr3:52526520-52526570	ProgFib	skin:	n/a
17	chr3:52526520-52526570	HUVEC	blood vessel:	n/a
18	chr3:52526520-52526570	AG04449	skin:	fetal
19	chr3:52526520-52526570	Caco-2	colon:	n/a
20	chr3:52526520-52526570	GM12878	blood:	n/a
21	chr3:52526520-52526570	ECC-1	luminal epithelium:	n/a
22	chr3:52526520-52526570	HL-60	blood:	n/a
23	chr3:52526520-52526570	HPAEpiC	pulmonary alveolar:	n/a
24	chr3:52526520-52526570	SK-N-SH_RA	brain:	n/a
25	chr3:52526520-52526570	BE2_C	brain:	n/a
26	chr3:52526520-52526570	NT2-D1	testis:	n/a
27	chr3:52526520-52526570	K562	blood:	n/a
28	chr3:52526520-52526570	HRPEpiC	eye:	n/a
29	chr3:52526520-52526570	HepG2	liver:	n/a
30	chr3:52526520-52526570	MCF10A-Er-Src	breast:	n/a
31	chr3:52526520-52526570	H1-hESC	embryonic stem cell:	embryo
32	chr3:52526520-52526570	NHDF-neo	bronchial:	n/a
33	chr3:52526520-52526570	LNCaP	prostate:	n/a
34	chr3:52526520-52526570	PANC-1	pancreas:	n/a
35	chr3:52526520-52526570	CMK	blood:	n/a
36	chr3:52526520-52526570	HAEpiC	amniotic membrane:	n/a
37	chr3:52526520-52526570	ovcar-3	ovarian:	n/a
38	chr3:52526520-52526570	GM19239	blood:	n/a
39	chr3:52526520-52526570	HCF	heart:	n/a
40	chr3:52526520-52526570	PrEC	prostate:	n/a
41	chr3:52526520-52526570	PFSK-1	brain:	n/a
42	chr3:52526520-52526570	Hela-S3	cervix:	n/a
43	chr3:52526520-52526570	AG10803	skin:	n/a
44	chr3:52526520-52526570	AG09309	skin:	n/a
45	chr3:52526520-52526570	AoSMC	blood vessel:	n/a
46	chr3:52526520-52526570	Jurkat	blood:	n/a
47	chr3:52526520-52526570	BJ	skin:	n/a
48	chr3:52526520-52526570	RPTEC	kidney:	n/a
49	chr3:52526520-52526570	HIPEpiC	eye:	n/a
50	chr3:52526520-52526570	HNPCEpiC	eye:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52525628..52528041-chr3:52561895..52563443,2	K562	blood:
2	chr3:52525356..52528300-chr3:52566814..52568456,2	MCF-7	breast:

No data

Variant related genes	Relation type
STAB1	TF binding region
STAB1	CpG island
ENSG00000168273	Chromatin interaction
ENSG00000168268	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2070914	1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs758800	1.00[CHB][hapmap];0.83[CHD][hapmap];0.85[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	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	esv1818902	chr3:52481406-52572056	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription 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 miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
7	nsv590304	chr3:52517206-52529266	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52491600-52528000	Strong transcription	Thymus	Thymus
2	chr3:52491800-52527000	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr3:52491800-52528200	Strong transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:52491800-52528200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:52493000-52527800	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr3:52498600-52527200	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr3:52499400-52527800	Strong transcription	Primary T cells from cord blood	blood
8	chr3:52499600-52529200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr3:52501600-52528800	Strong transcription	Fetal Intestine Small	intestine
10	chr3:52504200-52526600	Strong transcription	H9 Cell Line	embryonic stem cell
11	chr3:52504200-52526800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr3:52504200-52527400	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr3:52504200-52527400	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr3:52504200-52527600	Strong transcription	Dnd41	blood
15	chr3:52504200-52527800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:52504200-52528000	Strong transcription	Primary B cells from peripheral blood	blood
17	chr3:52504200-52528000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr3:52504200-52528600	Strong transcription	Brain Germinal Matrix	brain
19	chr3:52504400-52527400	Strong transcription	Osteobl	bone
20	chr3:52504400-52527600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:52504400-52527600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr3:52504400-52528000	Strong transcription	Fetal Brain Female	brain
23	chr3:52504800-52527400	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr3:52504800-52528000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr3:52505000-52527000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr3:52506400-52527400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:52507400-52527800	Strong transcription	Fetal Thymus	thymus
28	chr3:52508000-52532200	Weak transcription	K562	blood
29	chr3:52509400-52528000	Strong transcription	Gastric	stomach
30	chr3:52509600-52528200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr3:52510600-52528600	Weak transcription	Fetal Brain Male	brain
32	chr3:52511400-52528000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr3:52513400-52541400	Weak transcription	A549	lung
34	chr3:52513600-52530000	Weak transcription	Fetal Kidney	kidney
35	chr3:52514600-52534200	Weak transcription	Small Intestine	intestine
36	chr3:52515600-52528400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr3:52517200-52528200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr3:52518000-52526800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:52518600-52527200	Strong transcription	Muscle Satellite Cultured Cells	--
40	chr3:52518600-52527400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
41	chr3:52518600-52527400	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr3:52518800-52527000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:52518800-52527000	Strong transcription	HSMMtube	muscle
44	chr3:52518800-52527200	Strong transcription	NHEK	skin
45	chr3:52518800-52527600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr3:52518800-52527800	Strong transcription	Placenta Amnion	Placenta Amnion
47	chr3:52518800-52528000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr3:52518800-52528000	Strong transcription	Aorta	Aorta
49	chr3:52519000-52527400	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr3:52519000-52528200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links