Variant report

Variant	rs2788864
Chromosome Location	chr4:26416113-26416114
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:26320713..26323775-chr4:26414694..26418246,3	MCF-7	breast:
2	chr4:26369940..26371880-chr4:26414049..26416556,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168214	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10939110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10939111	0.82[CEU][hapmap]
rs13109703	0.85[CEU][hapmap]
rs13114911	0.85[CEU][hapmap]
rs13115260	0.80[CEU][hapmap]
rs2153155	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2270225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2725308	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3109828	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3109836	0.86[JPT][hapmap]
rs3109841	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3109844	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3113016	0.83[ASW][hapmap]
rs4618302	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6853254	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6853954	0.85[EUR][1000 genomes]
rs7349722	0.81[GIH][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2788864	PPARGC1A	cis	parietal	SCAN
rs2788864	PI4K2B	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26375200-26439200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:26381600-26439800	Weak transcription	Spleen	Spleen
3	chr4:26387200-26436000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr4:26399800-26437200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr4:26403000-26424800	Weak transcription	Fetal Brain Female	brain
6	chr4:26404400-26436000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr4:26404600-26418000	Weak transcription	Small Intestine	intestine
8	chr4:26408000-26439000	Weak transcription	Hela-S3	cervix
9	chr4:26408400-26422600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr4:26408400-26427000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:26408400-26428400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr4:26408400-26431000	Weak transcription	Fetal Kidney	kidney
13	chr4:26408400-26431400	Weak transcription	Esophagus	oesophagus
14	chr4:26408400-26442000	Weak transcription	Aorta	Aorta
15	chr4:26408600-26416400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr4:26408600-26417400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr4:26408600-26418000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr4:26408600-26422200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:26408600-26422600	Weak transcription	Thymus	Thymus
20	chr4:26408600-26425800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr4:26408600-26426800	Weak transcription	Brain Germinal Matrix	brain
22	chr4:26408600-26430800	Weak transcription	HUVEC	blood vessel
23	chr4:26408600-26430800	Weak transcription	K562	blood
24	chr4:26408800-26417400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr4:26408800-26417800	Weak transcription	HepG2	liver
26	chr4:26408800-26421600	Weak transcription	A549	lung
27	chr4:26408800-26421800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr4:26408800-26422200	Weak transcription	Primary B cells from peripheral blood	blood
29	chr4:26408800-26422200	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr4:26408800-26426600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr4:26408800-26432200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr4:26409000-26417000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr4:26409000-26417000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr4:26409000-26417200	Weak transcription	Fetal Intestine Large	intestine
35	chr4:26409000-26417200	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr4:26409000-26417200	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr4:26409000-26417400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr4:26409000-26422400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr4:26409000-26426000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr4:26409000-26431000	Weak transcription	NHEK	skin
41	chr4:26409000-26431600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr4:26409000-26431600	Weak transcription	HMEC	breast
43	chr4:26409200-26416800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr4:26409200-26416800	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr4:26409400-26416800	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr4:26409400-26416800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr4:26409800-26423400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr4:26410000-26417200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr4:26410400-26417600	Weak transcription	HSMMtube	muscle
50	chr4:26410600-26417000	Weak transcription	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links