Variant report

Variant	rs7612543
Chromosome Location	chr3:141158212-141158213
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:141028766..141032567-chr3:141157435..141160159,4	K562	blood:
2	chr3:141156646..141158952-chr3:141162167..141164221,2	K562	blood:
3	chr3:141112658..141115494-chr3:141157644..141160084,2	K562	blood:
4	chr3:141157834..141161364-chr3:141205126..141207553,3	K562	blood:
5	chr3:141157834..141161921-chr3:141205126..141207972,3	K562	blood:
6	chr3:141028495..141032567-chr3:141157435..141162053,7	K562	blood:
7	chr3:141087440..141090679-chr3:141157733..141160398,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000155903	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11711375	0.82[TSI][hapmap]
rs1366042	0.88[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.83[ASN][1000 genomes]
rs1582875	0.88[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs1863867	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs2042864	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs295320	0.82[TSI][hapmap]
rs3821710	0.82[TSI][hapmap]
rs6767158	0.84[TSI][hapmap]
rs6773734	0.84[ASN][1000 genomes]
rs6785874	0.82[TSI][hapmap]
rs6800122	0.82[TSI][hapmap]
rs6808837	0.82[TSI][hapmap]
rs7632308	0.88[CHB][hapmap];0.90[JPT][hapmap];0.84[TSI][hapmap];0.83[ASN][1000 genomes]
rs7643837	0.82[TSI][hapmap]
rs9289631	0.81[ASN][1000 genomes]
rs9813177	0.81[JPT][hapmap];0.82[TSI][hapmap]
rs9878347	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9879503	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][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	nsv829744	chr3:141016749-141189168	Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7612543	BPESC1	cis	parietal	SCAN
rs7612543	ZBTB38	cis	cerebellum	SCAN
rs7612543	ATP1B3	cis	cerebellum	SCAN
rs7612543	RASA2	cis	cerebellum	SCAN
rs7612543	GK5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141131800-141161200	Weak transcription	Thymus	Thymus
2	chr3:141132200-141171000	Weak transcription	Primary B cells from cord blood	blood
3	chr3:141133800-141158400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:141133800-141158400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:141134000-141161600	Weak transcription	Fetal Brain Male	brain
6	chr3:141134200-141161600	Weak transcription	Primary T cells from cord blood	blood
7	chr3:141135600-141160200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr3:141140800-141159200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:141145000-141160000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr3:141145400-141161200	Weak transcription	Fetal Brain Female	brain
11	chr3:141145400-141161800	Weak transcription	Esophagus	oesophagus
12	chr3:141145800-141161600	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr3:141146000-141160000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr3:141146000-141160000	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr3:141146000-141160000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr3:141146200-141160000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:141146600-141160000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr3:141147000-141161200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:141147000-141161200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:141147400-141160000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr3:141147800-141158400	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr3:141148600-141160000	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr3:141148800-141160000	Weak transcription	NHEK	skin
24	chr3:141148800-141161600	Weak transcription	Brain Germinal Matrix	brain
25	chr3:141148800-141161600	Weak transcription	Spleen	Spleen
26	chr3:141148800-141161800	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr3:141148800-141164200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr3:141149000-141158400	Weak transcription	HUVEC	blood vessel
29	chr3:141149400-141164200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:141149600-141161200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:141149800-141159000	Weak transcription	HMEC	breast
32	chr3:141149800-141160000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr3:141149800-141160000	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr3:141150800-141161200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr3:141151000-141160000	Weak transcription	Hela-S3	cervix
36	chr3:141152000-141158400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:141153000-141158400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:141153200-141161600	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr3:141153200-141164000	Weak transcription	Psoas Muscle	Psoas
40	chr3:141153400-141160400	Weak transcription	Right Atrium	heart
41	chr3:141153600-141160000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:141155000-141161400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:141155200-141158600	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr3:141155200-141159400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr3:141155400-141161200	Weak transcription	Liver	Liver
46	chr3:141155400-141170800	Weak transcription	Fetal Thymus	thymus
47	chr3:141155600-141159000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr3:141155800-141158600	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr3:141155800-141160200	Weak transcription	Small Intestine	intestine
50	chr3:141156000-141160000	Strong transcription	NHDF-Ad	bronchial

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