Variant report

Variant	rs1551248
Chromosome Location	chr2:173909277-173909278
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HA-E2F1	chr2:173909125-173909904	MCF-7	breast:	n/a	n/a
2	RAD21	chr2:173909012-173909905	MCF-7	breast:	n/a	n/a
3	MAX	chr2:173909075-173909905	MCF-7	breast:	n/a	n/a
4	GATA3	chr2:173909223-173910077	MCF-7	breast:	n/a	n/a
5	SIN3AK20	chr2:173908986-173910048	MCF-7	breast:	n/a	n/a
6	GATA3	chr2:173909263-173909995	MCF-7	breast:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:173908637..173910994-chr2:174830078..174831720,2	MCF-7	breast:
2	chr2:173903027..173904652-chr2:173908089..173910075,2	MCF-7	breast:
3	chr2:173908929..173910664-chr2:173926220..173928176,2	K562	blood:
4	chr2:173885808..173888407-chr2:173907815..173910951,3	MCF-7	breast:
5	chr2:173907898..173920360-chr2:173936226..173946823,30	MCF-7	breast:
6	chr13:29291574..29294456-chr2:173907850..173910644,2	MCF-7	breast:
7	chr2:173895149..173898676-chr2:173907706..173911844,6	MCF-7	breast:
8	chr2:173905270..173911343-chr2:173911871..173916630,12	MCF-7	breast:
9	chr2:173907933..173910689-chr2:173917476..173919133,2	K562	blood:

No data

Variant related genes	Relation type
RAPGEF4	TF binding region
ENSG00000091436	Chromatin interaction
ENSG00000091428	Chromatin interaction
ENSG00000265709	Chromatin interaction
ENSG00000139508	Chromatin interaction
ENSG00000172845	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10187560	0.90[CEU][hapmap]
rs1020599	0.85[CEU][hapmap]
rs12474338	0.84[ASN][1000 genomes]
rs1551249	0.84[CEU][hapmap];0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs1973037	0.84[CEU][hapmap];0.82[ASN][1000 genomes]
rs2012213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3769210	1.00[CEU][hapmap];0.80[CHB][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3769211	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3769213	0.84[CEU][hapmap];0.84[ASN][1000 genomes]
rs60121307	0.81[ASN][1000 genomes]
rs6717529	0.84[CEU][hapmap]
rs6717735	0.84[CEU][hapmap]
rs6742219	0.87[CEU][hapmap];0.84[ASN][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	nsv834459	chr2:173735192-173926750	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173881200-173912800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:173893000-173913200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr2:173893200-173922000	Weak transcription	Brain Anterior Caudate	brain
4	chr2:173901000-173918000	Weak transcription	Brain Angular Gyrus	brain
5	chr2:173902400-173909600	Weak transcription	Small Intestine	intestine
6	chr2:173902800-173909800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr2:173904400-173921400	Weak transcription	Ovary	ovary
8	chr2:173904600-173913000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr2:173906400-173910200	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr2:173906800-173912800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr2:173906800-173913000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:173907400-173909400	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr2:173907600-173910400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr2:173907800-173910400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:173908000-173910600	Enhancers	Rectal Smooth Muscle	rectum
16	chr2:173908200-173910000	Enhancers	HMEC	breast
17	chr2:173908400-173909400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:173908400-173909600	Enhancers	K562	blood
19	chr2:173908400-173910000	Enhancers	Placenta	Placenta
20	chr2:173908400-173910600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:173908400-173910600	Enhancers	NHLF	lung
22	chr2:173908600-173909600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr2:173908600-173909800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr2:173908600-173910000	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr2:173908600-173916800	Enhancers	Fetal Intestine Large	intestine
26	chr2:173908600-173921400	Weak transcription	Left Ventricle	heart
27	chr2:173908800-173909600	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr2:173908800-173909800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr2:173908800-173911200	Weak transcription	Fetal Heart	heart
30	chr2:173908800-173912800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr2:173908800-173912800	Weak transcription	Stomach Mucosa	stomach
32	chr2:173908800-173914400	Weak transcription	Liver	Liver
33	chr2:173908800-173924200	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr2:173909000-173912800	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr2:173909000-173916800	Enhancers	Fetal Intestine Small	intestine
36	chr2:173909200-173910000	Enhancers	H9 Cell Line	embryonic stem cell
37	chr2:173909200-173910200	Enhancers	Colon Smooth Muscle	Colon
38	chr2:173909200-173910400	Enhancers	Fetal Stomach	stomach
39	chr2:173909200-173910600	Enhancers	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links