Variant report

Variant	rs9789538
Chromosome Location	chr2:172618474-172618475
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:172608374..172611206-chr2:172617734..172620061,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1028127	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10930491	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11690807	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12052995	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12997093	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12998411	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1607254	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17581284	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17614941	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2271758	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2292816	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34242651	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34531723	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35854151	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3770458	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4510184	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs59844139	0.83[AMR][1000 genomes]
rs62184165	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6723259	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[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	nsv834457	chr2:172564939-172770901	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9789538	AC068039.4	cis	Thyroid	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172569000-172618600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:172587800-172640800	Weak transcription	Psoas Muscle	Psoas
3	chr2:172588400-172619800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:172593200-172645000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:172595400-172619000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr2:172602000-172624200	Weak transcription	Esophagus	oesophagus
7	chr2:172602600-172621800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr2:172603000-172688400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr2:172603400-172621200	Weak transcription	Small Intestine	intestine
10	chr2:172604400-172618600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr2:172604400-172641200	Weak transcription	Colon Smooth Muscle	Colon
12	chr2:172605600-172622400	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr2:172605800-172620600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr2:172606200-172620000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr2:172606400-172619400	Weak transcription	NHEK	skin
16	chr2:172607400-172627000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr2:172607600-172618800	Weak transcription	Fetal Kidney	kidney
18	chr2:172607600-172619200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr2:172608800-172619600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:172609000-172622200	Weak transcription	Fetal Brain Male	brain
21	chr2:172609200-172620400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr2:172609600-172628800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr2:172609800-172618600	Weak transcription	HepG2	liver
24	chr2:172609800-172620600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr2:172610000-172619200	Weak transcription	Brain Substantia Nigra	brain
26	chr2:172610200-172618800	Weak transcription	NHLF	lung
27	chr2:172610200-172651400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr2:172610400-172620000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr2:172610600-172619600	Weak transcription	HMEC	breast
30	chr2:172610800-172619600	Weak transcription	Brain Hippocampus Middle	brain
31	chr2:172611200-172618600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr2:172611200-172619400	Weak transcription	HUVEC	blood vessel
33	chr2:172611400-172618800	Weak transcription	HSMMtube	muscle
34	chr2:172611400-172618800	Weak transcription	NHDF-Ad	bronchial
35	chr2:172614800-172619200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr2:172615400-172623800	Weak transcription	Fetal Lung	lung
37	chr2:172616000-172618800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr2:172616000-172619000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:172616200-172619400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr2:172616400-172619400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr2:172616400-172619400	Strong transcription	Fetal Muscle Leg	muscle
42	chr2:172616400-172620400	Strong transcription	Fetal Muscle Trunk	muscle
43	chr2:172616600-172619000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr2:172616600-172619200	Strong transcription	Brain Germinal Matrix	brain
45	chr2:172616600-172619200	Strong transcription	Fetal Brain Female	brain
46	chr2:172616600-172619200	Strong transcription	Stomach Smooth Muscle	stomach
47	chr2:172616600-172619400	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr2:172616600-172619800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr2:172616800-172618800	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr2:172616800-172619000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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