Variant report

Variant	rs12422905
Chromosome Location	chr12:9107673-9107674
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	chr12:9102147..9104333-chr12:9105347..9108888,4	MCF-7	breast:
2	chr12:9102428..9104198-chr12:9107371..9109870,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000003056	Chromatin interaction
ENSG00000139187	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1049925	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10842537	0.82[EUR][1000 genomes]
rs10842660	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10842662	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11047953	0.82[EUR][1000 genomes]
rs11048023	0.86[EUR][1000 genomes]
rs11048190	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11048195	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11048264	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11048337	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11048338	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11048344	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11048345	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1124402	0.81[EUR][1000 genomes]
rs11494569	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11494570	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11611106	0.81[EUR][1000 genomes]
rs11613650	0.81[EUR][1000 genomes]
rs11614202	0.82[ASN][1000 genomes]
rs12371786	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12423746	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12423817	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12424026	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12581860	0.82[AMR][1000 genomes]
rs12812913	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12814670	0.81[EUR][1000 genomes]
rs12815310	0.81[EUR][1000 genomes]
rs12820395	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12821842	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12823100	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12824140	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12824380	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12827055	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12827988	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12828902	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12833375	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1476911	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1805248	0.83[ASN][1000 genomes]
rs1805721	0.81[EUR][1000 genomes]
rs1805722	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1805723	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1805724	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1805725	0.82[ASN][1000 genomes]
rs1805727	0.82[ASN][1000 genomes]
rs1805732	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1805733	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1805736	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1805737	0.89[EUR][1000 genomes]
rs1805745	0.82[EUR][1000 genomes]
rs1805761	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1805765	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1805784	0.82[EUR][1000 genomes]
rs2041624	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2041625	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2080116	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2080117	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2110190	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2110191	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2110192	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2110193	0.81[EUR][1000 genomes]
rs2159961	0.81[EUR][1000 genomes]
rs2377672	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2377673	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2377674	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34285491	0.99[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34798934	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35870866	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4254119	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4309200	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7300767	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7301381	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7302417	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7303776	0.81[EUR][1000 genomes]
rs7309922	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7314942	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7315055	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7957321	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs933462	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[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	nsv832327	chr12:9081779-9246220	Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12422905	KLRG1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9103000-9109400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:9103400-9112000	Weak transcription	Pancreas	Pancrea
3	chr12:9103400-9116400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:9103600-9110400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr12:9103600-9114000	Weak transcription	Fetal Kidney	kidney
6	chr12:9103600-9114200	Weak transcription	Aorta	Aorta
7	chr12:9103600-9114400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr12:9103600-9114600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr12:9104000-9108400	Weak transcription	Fetal Muscle Leg	muscle
10	chr12:9104000-9108400	Weak transcription	Right Ventricle	heart
11	chr12:9104000-9108600	Weak transcription	Fetal Stomach	stomach
12	chr12:9104000-9108600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr12:9104000-9108800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:9104000-9110400	Weak transcription	A549	lung
15	chr12:9104000-9111000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr12:9104000-9113200	Weak transcription	HepG2	liver
17	chr12:9104000-9114400	Weak transcription	Psoas Muscle	Psoas
18	chr12:9104400-9111200	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr12:9104600-9110400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr12:9104600-9113800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr12:9104800-9109600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
22	chr12:9105000-9108400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:9105000-9108800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr12:9105000-9113600	Weak transcription	Primary B cells from peripheral blood	blood
25	chr12:9105000-9113800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr12:9106000-9108400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr12:9106200-9108000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr12:9106200-9108400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr12:9106600-9108200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr12:9106600-9108400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr12:9106600-9108400	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr12:9106600-9108600	Weak transcription	Primary B cells from cord blood	blood
33	chr12:9106600-9109400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr12:9106600-9116000	Weak transcription	Left Ventricle	heart
35	chr12:9106800-9108000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr12:9106800-9108200	Weak transcription	Primary hematopoietic stem cells	blood
37	chr12:9106800-9108400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr12:9106800-9108400	Weak transcription	Thymus	Thymus
39	chr12:9106800-9108600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr12:9106800-9109400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr12:9106800-9110600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr12:9106800-9112200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr12:9106800-9114400	Enhancers	Primary T cells fromperipheralblood	blood
44	chr12:9106800-9114600	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr12:9107000-9107800	Strong transcription	Liver	Liver
46	chr12:9107000-9108000	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr12:9107000-9110200	Weak transcription	Brain Hippocampus Middle	brain
48	chr12:9107000-9111200	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr12:9107200-9112800	Enhancers	Primary T cells from cord blood	blood
50	chr12:9107200-9112800	Enhancers	Primary T helper naive cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links