Variant report

Variant	rs2288372
Chromosome Location	chr3:42978032-42978033
allele	C/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:1)
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	GABPA	chr3:42977640-42978515	K562	blood:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:42978026-42978076	NH-A	brain:	n/a
2	chr3:42978026-42978076	GM12891	blood:	n/a
3	chr3:42978026-42978076	HIPEpiC	eye:	n/a
4	chr3:42978026-42978076	GM12878	blood:	n/a
5	chr3:42978026-42978076	HPAEpiC	pulmonary alveolar:	n/a
6	chr3:42978026-42978076	AG09319	gingival:	n/a
7	chr3:42978026-42978076	AoSMC	blood vessel:	n/a
8	chr3:42978026-42978076	AG04450	lung:	fetal
9	chr3:42978026-42978076	HepG2	liver:	n/a
10	chr3:42978026-42978076	LNCaP	prostate:	n/a
11	chr3:42978026-42978076	ProgFib	skin:	n/a
12	chr3:42978026-42978076	AG09309	skin:	n/a
13	chr3:42978026-42978076	SKMC	muscle:	n/a
14	chr3:42978026-42978076	HCF	heart:	n/a
15	chr3:42978026-42978076	GM12892	blood:	n/a
16	chr3:42978026-42978076	AG10803	skin:	n/a
17	chr3:42978026-42978076	HL-60	blood:	n/a
18	chr3:42978026-42978076	A549	lung:	n/a
19	chr3:42978026-42978076	HEEpiC	esophagus:	n/a
20	chr3:42978026-42978076	IMR90	lung:	fetal
21	chr3:42978026-42978076	SK-N-SH_RA	brain:	n/a
22	chr3:42978026-42978076	SK-N-SH	brain:	n/a
23	chr3:42978026-42978076	HCT-116	colon:	n/a
24	chr3:42978026-42978076	BJ	skin:	n/a
25	chr3:42978026-42978076	RPTEC	kidney:	n/a
26	chr3:42978026-42978076	CMK	blood:	n/a
27	chr3:42978026-42978076	T-47D	breast:	n/a
28	chr3:42978026-42978076	BE2_C	brain:	n/a
29	chr3:42978026-42978076	U87	brain:	n/a
30	chr3:42978026-42978076	HEK293	kidney:	embryo
31	chr3:42978026-42978076	NT2-D1	testis:	n/a
32	chr3:42978026-42978076	MCF10A-Er-Src	breast:	n/a
33	chr3:42978026-42978076	GM19239	blood:	n/a
34	chr3:42978026-42978076	HNPCEpiC	eye:	n/a
35	chr3:42978026-42978076	Hela-S3	cervix:	n/a
36	chr3:42978026-42978076	H1-hESC	embryonic stem cell:	embryo
37	chr3:42978026-42978076	HUVEC	blood vessel:	n/a
38	chr3:42978026-42978076	Hepatocyte	liver:	n/a
39	chr3:42978026-42978076	MCF-7	breast:	n/a
40	chr3:42978026-42978076	NB4	blood:	n/a
41	chr3:42978026-42978076	NHBE	bronchial:	n/a
42	chr3:42978026-42978076	Caco-2	colon:	n/a
43	chr3:42978026-42978076	PrEC	prostate:	n/a
44	chr3:42978026-42978076	PFSK-1	brain:	n/a
45	chr3:42978026-42978076	GM06990	blood:	n/a
46	chr3:42978026-42978076	HAEpiC	amniotic membrane:	n/a
47	chr3:42978026-42978076	HMEC	breast:	n/a
48	chr3:42978026-42978076	HCM	heart:	n/a
49	chr3:42978026-42978076	HRPEpiC	eye:	n/a
50	chr3:42978026-42978076	NHDF-neo	bronchial:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42976404..42980028-chr3:42981618..42984060,3	K562	blood:
2	chr3:42977585..42980028-chr3:42981618..42983637,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CYP8B1-1	chr3:42977249-42978277	ENSG00000206552

No data

Variant related genes	Relation type
ENSG00000273291	TF binding region
KRBOX1	TF binding region
ENSG00000273291	CpG island
KRBOX1	CpG island
ENSG00000240747	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11129987	0.87[ASN][1000 genomes]
rs11129988	0.87[ASN][1000 genomes]
rs2288371	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2288373	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs542394	1.00[JPT][hapmap]
rs545023	1.00[JPT][hapmap]
rs59789275	0.83[ASN][1000 genomes]
rs60046829	0.83[ASN][1000 genomes]
rs60607395	0.83[ASN][1000 genomes]
rs61102947	0.83[ASN][1000 genomes]
rs619660	1.00[JPT][hapmap]
rs6778645	0.91[ASN][1000 genomes]
rs6779194	0.83[ASN][1000 genomes]
rs6798520	1.00[JPT][hapmap]
rs704895	0.81[ASN][1000 genomes]
rs7621158	0.83[ASN][1000 genomes]
rs7625959	1.00[JPT][hapmap]
rs834579	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs834584	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9874514	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460522	chr3:42967597-43175207	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv590149	chr3:42967597-43175207	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42962400-42980400	Weak transcription	Placenta	Placenta
2	chr3:42975800-42978200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr3:42976000-42978200	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr3:42977000-42978600	Active TSS	Brain Anterior Caudate	brain
5	chr3:42977200-42978200	Enhancers	Primary T cells from cord blood	blood
6	chr3:42977200-42978200	Active TSS	Brain Angular Gyrus	brain
7	chr3:42977200-42978400	Active TSS	Brain Hippocampus Middle	brain
8	chr3:42977200-42978400	Active TSS	Stomach Smooth Muscle	stomach
9	chr3:42977400-42978200	Active TSS	Brain Cingulate Gyrus	brain
10	chr3:42977400-42978200	Active TSS	Fetal Lung	lung
11	chr3:42977400-42978400	Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr3:42977400-42978400	Active TSS	Adipose Nuclei	Adipose
13	chr3:42977400-42978400	Active TSS	Brain Germinal Matrix	brain
14	chr3:42977400-42978400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:42977400-42978400	Active TSS	Colon Smooth Muscle	Colon
16	chr3:42977400-42978400	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
17	chr3:42977400-42978400	Active TSS	Fetal Intestine Small	intestine
18	chr3:42977400-42978400	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr3:42977400-42978400	Active TSS	Right Atrium	heart
20	chr3:42977400-42978400	Active TSS	NHDF-Ad	bronchial
21	chr3:42977400-42978600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr3:42977400-42978600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:42977400-42978600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:42977400-42978600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr3:42977400-42978600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:42977400-42978600	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr3:42977400-42978600	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr3:42977400-42978600	Active TSS	Fetal Kidney	kidney
29	chr3:42977400-42978600	Active TSS	Osteobl	bone
30	chr3:42977600-42978200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:42977600-42978200	Active TSS	Muscle Satellite Cultured Cells	--
32	chr3:42977600-42978200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:42977600-42978200	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr3:42977600-42978200	Active TSS	Aorta	Aorta
35	chr3:42977600-42978200	Active TSS	Colonic Mucosa	Colon
36	chr3:42977600-42978200	Active TSS	Duodenum Mucosa	Duodenum
37	chr3:42977600-42978200	Active TSS	Esophagus	oesophagus
38	chr3:42977600-42978200	Bivalent/Poised TSS	Left Ventricle	heart
39	chr3:42977600-42978200	Active TSS	Psoas Muscle	Psoas
40	chr3:42977600-42978200	Active TSS	Right Ventricle	heart
41	chr3:42977600-42978200	Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr3:42977600-42978200	Active TSS	HSMM	muscle
43	chr3:42977600-42978400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:42977600-42978400	Active TSS	Brain Substantia Nigra	brain
45	chr3:42977600-42978400	Active TSS	Fetal Intestine Large	intestine
46	chr3:42977600-42978400	Active TSS	Fetal Muscle Leg	muscle
47	chr3:42977600-42978400	Active TSS	Fetal Stomach	stomach
48	chr3:42977600-42978400	Active TSS	Rectal Smooth Muscle	rectum
49	chr3:42977600-42978400	Active TSS	HSMMtube	muscle
50	chr3:42977600-42978400	Active TSS	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links