Variant report

Variant	rs1492897
Chromosome Location	chr12:46625414-46625415
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46623253..46626164-chr12:46632667..46635134,2	K562	blood:
2	chr12:46624577..46626777-chr12:46651581..46654334,2	MCF-7	breast:
3	chr12:46623492..46625436-chr12:46629960..46632352,2	MCF-7	breast:
4	chr12:46618211..46621572-chr12:46623361..46625417,5	K562	blood:
5	chr12:46618654..46626602-chr12:46659026..46664546,12	MCF-7	breast:
6	chr12:46623524..46627922-chr12:46630089..46633482,4	K562	blood:
7	chr12:46624985..46628794-chr12:46656283..46658720,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111371	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1000405	0.84[EUR][1000 genomes]
rs10880944	0.90[EUR][1000 genomes]
rs11504510	0.90[EUR][1000 genomes]
rs12299843	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs12303214	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs12580460	0.90[EUR][1000 genomes]
rs1492893	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs2408495	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3847985	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs4445700	0.90[EUR][1000 genomes]
rs4768109	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs4768692	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs4768693	0.83[EUR][1000 genomes]
rs56988021	0.90[EUR][1000 genomes]
rs7312682	0.90[EUR][1000 genomes]
rs7957777	0.94[EUR][1000 genomes]
rs7959095	0.90[EUR][1000 genomes]
rs7960819	0.94[EUR][1000 genomes]
rs7967629	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs7971312	0.88[EUR][1000 genomes]
rs973988	0.92[CEU][hapmap]

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	nsv832398	chr12:46611692-46825530	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	181 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46592800-46654200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:46597600-46659600	Weak transcription	Colonic Mucosa	Colon
3	chr12:46604000-46633800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:46604000-46637400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:46610600-46640000	Weak transcription	Esophagus	oesophagus
6	chr12:46613800-46639800	Weak transcription	Lung	lung
7	chr12:46614400-46627400	Weak transcription	Right Ventricle	heart
8	chr12:46615600-46632400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr12:46615600-46636600	Weak transcription	Brain Anterior Caudate	brain
10	chr12:46615800-46637800	Weak transcription	Dnd41	blood
11	chr12:46615800-46653800	Weak transcription	NH-A	brain
12	chr12:46616000-46640600	Strong transcription	Fetal Thymus	thymus
13	chr12:46616000-46650400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr12:46616200-46636600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr12:46616400-46637200	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr12:46616400-46637800	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr12:46616400-46653600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr12:46616800-46627200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr12:46616800-46638600	Strong transcription	HMEC	breast
20	chr12:46616800-46639800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr12:46616800-46641600	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr12:46617000-46636800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr12:46617000-46637800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
24	chr12:46617000-46653000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr12:46617200-46636200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr12:46617200-46639000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:46617200-46640200	Strong transcription	Hela-S3	cervix
28	chr12:46618400-46632200	Weak transcription	Brain Germinal Matrix	brain
29	chr12:46618400-46639800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr12:46618400-46639800	Weak transcription	Spleen	Spleen
31	chr12:46618400-46641400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr12:46618400-46653800	Weak transcription	HSMMtube	muscle
33	chr12:46618600-46626200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr12:46618600-46634200	Weak transcription	Fetal Stomach	stomach
35	chr12:46618600-46639800	Weak transcription	Aorta	Aorta
36	chr12:46618800-46628800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr12:46618800-46633200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr12:46619200-46627400	Weak transcription	Stomach Smooth Muscle	stomach
39	chr12:46619200-46638800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr12:46619400-46639800	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr12:46619600-46631400	Weak transcription	Fetal Muscle Leg	muscle
42	chr12:46619600-46633400	Weak transcription	Left Ventricle	heart
43	chr12:46619600-46638200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:46619600-46639800	Weak transcription	Psoas Muscle	Psoas
45	chr12:46620400-46636400	Strong transcription	GM12878-XiMat	blood
46	chr12:46620600-46627800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr12:46620800-46625600	Weak transcription	Fetal Intestine Small	intestine
48	chr12:46621000-46627800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr12:46621200-46626000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr12:46621200-46626200	Strong transcription	HSMM	muscle

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