Variant report

Variant	rs1547710
Chromosome Location	chr13:52001985-52001986
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
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	STAT3	chr13:52001718-52002004	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:52001846..52004227-chr13:52025679..52027392,2	MCF-7	breast:
2	chr13:51998975..52003064-chr13:52024296..52027890,4	K562	blood:
3	chr13:52001566..52003348-chr13:52376076..52378934,2	MCF-7	breast:
4	chr13:51996691..52002238-chr13:52025569..52028541,7	MCF-7	breast:
5	chr13:52000192..52002988-chr13:52004718..52007508,2	K562	blood:
6	chr13:52000566..52003254-chr13:52016445..52019373,2	K562	blood:
7	chr13:52000304..52002866-chr13:52009903..52011496,2	K562	blood:

No data

Variant related genes	Relation type
INTS6	TF binding region
ENSG00000102786	Chromatin interaction
ENSG00000224892	Chromatin interaction
ENSG00000231856	Chromatin interaction
ENSG00000236778	Chromatin interaction
ENSG00000102796	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11148219	0.82[JPT][hapmap]
rs17252166	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17252173	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17252180	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17252193	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17252200	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17837214	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17837215	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17837216	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17837217	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4941699	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs4942995	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs4942996	0.82[JPT][hapmap]
rs4942999	0.82[JPT][hapmap]
rs57845363	0.81[ASN][1000 genomes]
rs61749884	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61749885	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7330735	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74087486	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7984158	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7992891	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs7995478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7995885	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8000429	1.00[CHB][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8000433	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8001333	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8002112	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9563049	0.82[JPT][hapmap]
rs9563055	0.82[JPT][hapmap]
rs9568580	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs9568586	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs9568631	0.86[CHB][hapmap]
rs9568632	1.00[AMR][1000 genomes]
rs9591402	0.82[JPT][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1547710	Hs.123474	cis	multi-tissue	Pritchard

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51945800-52016600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr13:51949400-52025000	Weak transcription	Fetal Muscle Leg	muscle
3	chr13:51950000-52025200	Weak transcription	Fetal Muscle Trunk	muscle
4	chr13:51963200-52024800	Weak transcription	Fetal Intestine Large	intestine
5	chr13:51963600-52003600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr13:51971800-52025000	Weak transcription	Fetal Stomach	stomach
7	chr13:51972000-52005200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr13:51972000-52016000	Weak transcription	Pancreas	Pancrea
9	chr13:51978400-52003200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr13:51984400-52024800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr13:51988800-52024400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr13:51990000-52016600	Weak transcription	Fetal Intestine Small	intestine
13	chr13:51990800-52003200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr13:51991400-52003200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr13:51991400-52006200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr13:51992400-52025400	Weak transcription	Esophagus	oesophagus
17	chr13:51992600-52002200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr13:51993000-52002200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr13:51993600-52003600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr13:51994600-52002200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr13:51994600-52005600	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr13:51995400-52002000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr13:51995400-52002800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr13:51995400-52023400	Weak transcription	Fetal Kidney	kidney
25	chr13:51995400-52024600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr13:51995600-52002000	Weak transcription	Fetal Thymus	thymus
27	chr13:51995600-52002600	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr13:51995600-52002800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr13:51995600-52003600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr13:51995600-52019000	Weak transcription	Gastric	stomach
31	chr13:51995600-52023400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr13:51995600-52025000	Weak transcription	Right Ventricle	heart
33	chr13:51995600-52025600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr13:51995800-52008000	Weak transcription	Hela-S3	cervix
35	chr13:51996600-52002200	Enhancers	Pancreatic Islets	Pancreatic Islet
36	chr13:51996800-52002000	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr13:51997000-52003200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr13:51997000-52007200	Weak transcription	Psoas Muscle	Psoas
39	chr13:51997000-52025200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr13:51997200-52003800	Weak transcription	HMEC	breast
41	chr13:51997400-52002000	Weak transcription	Dnd41	blood
42	chr13:51997400-52003200	Weak transcription	HUVEC	blood vessel
43	chr13:51997400-52024400	Weak transcription	Thymus	Thymus
44	chr13:51997600-52003800	Weak transcription	K562	blood
45	chr13:51997600-52006600	Weak transcription	Fetal Heart	heart
46	chr13:51997600-52023200	Weak transcription	Primary hematopoietic stem cells	blood
47	chr13:51997600-52023600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr13:51997800-52002600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr13:51998000-52002200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr13:51998200-52002400	Strong transcription	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links