Variant report

Variant	rs2577838
Chromosome Location	chr3:52718446-52718447
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	MXI1	chr3:52717818-52721863	SK-N-SH	brain:	n/a	n/a
2	ZNF384	chr3:52718108-52718568	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:52718446-52723739	IMR90	lung:	n/a	n/a
4	POLR2A	chr3:52718374-52724293	MCF10A-Er-Src	breast:	n/a	n/a
5	ARID3A	chr3:52718139-52718564	HepG2	liver:	n/a	n/a
6	HCFC1	chr3:52717761-52720928	Hela-S3	cervix:	n/a	n/a
7	STAT3	chr3:52718377-52718533	MCF10A-Er-Src	breast:	n/a	n/a
8	CHD1	chr3:52718172-52721742	IMR90	lung:	n/a	chr3:52719550-52719557

No.	Distal block	Cell Line	Cell type
1	chr3:52567553..52570571-chr3:52718365..52721514,3	MCF-7	breast:
2	chr3:52443115..52446014-chr3:52718098..52719635,2	K562	blood:
3	chr3:52568115..52572187-chr3:52717267..52721555,8	K562	blood:
4	chr3:52712073..52717938-chr3:52718038..52722104,14	K562	blood:
5	chr3:52701409..52703551-chr3:52716024..52719023,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000252787	TF binding region
PBRM1	TF binding region
GNL3	TF binding region
SNORD19	TF binding region
ENSG00000163939	Chromatin interaction
ENSG00000163938	Chromatin interaction
ENSG00000163930	Chromatin interaction
ENSG00000168268	Chromatin interaction
ENSG00000168273	Chromatin interaction
ENSG00000010318	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs17052326	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17052421	0.87[AFR][1000 genomes]
rs2577828	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2577830	1.00[AMR][1000 genomes]
rs2590840	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2590841	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34296002	1.00[AMR][1000 genomes]
rs4234635	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72947530	0.83[AFR][1000 genomes]
rs72947531	0.83[AFR][1000 genomes]
rs72947532	0.83[AFR][1000 genomes]
rs72947537	0.80[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52587200-52719200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:52592200-52719200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:52665400-52719200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:52712600-52719400	Weak transcription	Gastric	stomach
5	chr3:52713200-52719200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:52713600-52718600	Enhancers	Adipose Nuclei	Adipose
7	chr3:52713600-52719200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:52713800-52719200	Weak transcription	Aorta	Aorta
9	chr3:52714200-52718600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:52714200-52718800	Weak transcription	Right Atrium	heart
11	chr3:52714200-52718800	Weak transcription	Right Ventricle	heart
12	chr3:52714200-52719200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:52714200-52719200	Weak transcription	Esophagus	oesophagus
14	chr3:52714200-52719400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:52714400-52718600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr3:52714400-52718800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr3:52714600-52718600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr3:52714800-52718800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:52714800-52719000	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr3:52715200-52719000	Weak transcription	Placenta	Placenta
21	chr3:52715200-52719400	Weak transcription	Spleen	Spleen
22	chr3:52715400-52718600	Weak transcription	Psoas Muscle	Psoas
23	chr3:52715600-52718600	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr3:52715800-52718800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr3:52715800-52719000	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr3:52716000-52718800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr3:52716200-52719000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr3:52716200-52719200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:52716400-52718600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr3:52716600-52718600	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr3:52716600-52718600	Weak transcription	A549	lung
32	chr3:52716800-52718600	Enhancers	Monocytes-CD14+_RO01746	blood
33	chr3:52716800-52718800	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr3:52716800-52718800	Enhancers	Primary T cells fromperipheralblood	blood
35	chr3:52716800-52719200	Weak transcription	Ovary	ovary
36	chr3:52716800-52719400	Weak transcription	Small Intestine	intestine
37	chr3:52717200-52718600	Enhancers	Primary T cells from cord blood	blood
38	chr3:52717200-52718600	Enhancers	Brain Hippocampus Middle	brain
39	chr3:52717200-52718800	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr3:52717400-52718600	Enhancers	Fetal Heart	heart
41	chr3:52717400-52718800	Enhancers	Primary B cells from cord blood	blood
42	chr3:52717600-52718600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:52717600-52718600	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr3:52717600-52718600	Enhancers	Fetal Lung	lung
45	chr3:52717600-52718600	Enhancers	Fetal Muscle Leg	muscle
46	chr3:52717600-52718600	Enhancers	Rectal Mucosa Donor 29	rectum
47	chr3:52717600-52718600	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr3:52717600-52718600	Enhancers	Stomach Smooth Muscle	stomach
49	chr3:52717600-52718800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr3:52717600-52718800	Enhancers	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links