Variant report

Variant	rs12299477
Chromosome Location	chr12:50084863-50084864
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	chr12:50080143..50085132-chr12:50089232..50093203,6	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10128824	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11169071	1.00[EUR][1000 genomes]
rs11169110	1.00[ASW][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11169114	1.00[ASW][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11169115	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11169120	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11169123	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11831670	1.00[EUR][1000 genomes]
rs11835085	1.00[EUR][1000 genomes]
rs12297814	1.00[ASW][hapmap];0.93[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12298123	1.00[EUR][1000 genomes]
rs12299666	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12299743	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12299751	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12300085	1.00[EUR][1000 genomes]
rs12300919	0.83[AFR][1000 genomes]
rs12300962	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12306942	1.00[EUR][1000 genomes]
rs12306951	1.00[AMR][1000 genomes]
rs12309399	1.00[EUR][1000 genomes]
rs12310580	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12311319	1.00[EUR][1000 genomes]
rs12311910	1.00[EUR][1000 genomes]
rs12312112	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12313583	1.00[EUR][1000 genomes]
rs12313657	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12313681	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12314036	1.00[ASW][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12314348	1.00[EUR][1000 genomes]
rs12315508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12315746	1.00[EUR][1000 genomes]
rs12315941	1.00[EUR][1000 genomes]
rs12317162	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12319527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12320104	1.00[EUR][1000 genomes]
rs12320612	1.00[EUR][1000 genomes]
rs12320895	1.00[ASW][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12321717	1.00[EUR][1000 genomes]
rs1317263	1.00[AMR][1000 genomes]
rs17119738	0.88[MKK][hapmap];1.00[AMR][1000 genomes]
rs17123787	1.00[AMR][1000 genomes]
rs17123827	1.00[AMR][1000 genomes]
rs17123879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17123924	1.00[ASW][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28420769	1.00[EUR][1000 genomes]
rs57970210	1.00[EUR][1000 genomes]
rs58867453	1.00[EUR][1000 genomes]
rs59570650	1.00[EUR][1000 genomes]
rs59576871	1.00[EUR][1000 genomes]
rs60507124	1.00[EUR][1000 genomes]
rs61227990	1.00[EUR][1000 genomes]
rs7960185	1.00[EUR][1000 genomes]
rs9804867	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9805090	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50077400-50086200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr12:50078000-50087600	Weak transcription	Placenta	Placenta
3	chr12:50078000-50091000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr12:50078600-50090600	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr12:50078600-50092200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr12:50078800-50088200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr12:50078800-50088200	Weak transcription	HSMM	muscle
8	chr12:50078800-50091800	Weak transcription	NH-A	brain
9	chr12:50078800-50092400	Weak transcription	NHLF	lung
10	chr12:50079000-50088000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr12:50079000-50088000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr12:50079000-50092000	Weak transcription	Small Intestine	intestine
13	chr12:50079000-50096200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr12:50079200-50090600	Weak transcription	Ovary	ovary
15	chr12:50079200-50091000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr12:50079200-50092400	Weak transcription	Fetal Stomach	stomach
17	chr12:50079200-50092800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr12:50079400-50088000	Weak transcription	HSMMtube	muscle
19	chr12:50079400-50090600	Weak transcription	Psoas Muscle	Psoas
20	chr12:50080800-50092800	Weak transcription	Fetal Muscle Trunk	muscle
21	chr12:50081600-50085600	Enhancers	Primary B cells from peripheral blood	blood
22	chr12:50082000-50085200	Enhancers	Primary T cells from cord blood	blood
23	chr12:50082000-50088000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr12:50082000-50088200	Weak transcription	Osteobl	bone
25	chr12:50082000-50092800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr12:50082200-50090000	Weak transcription	Left Ventricle	heart
27	chr12:50082200-50092000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:50082200-50092800	Weak transcription	Aorta	Aorta
29	chr12:50082400-50085400	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr12:50082400-50086200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr12:50082400-50086400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:50082600-50085000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr12:50082600-50085000	Enhancers	Primary B cells from cord blood	blood
34	chr12:50082800-50085400	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr12:50083000-50085200	Flanking Active TSS	GM12878-XiMat	blood
36	chr12:50083000-50085400	Enhancers	Fetal Muscle Leg	muscle
37	chr12:50083200-50085200	Enhancers	Fetal Lung	lung
38	chr12:50083200-50085800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr12:50083400-50085000	Enhancers	Stomach Mucosa	stomach
40	chr12:50083400-50085600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr12:50083400-50092800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr12:50083600-50089200	Weak transcription	Brain Cingulate Gyrus	brain
43	chr12:50083600-50092800	Weak transcription	Lung	lung
44	chr12:50083800-50087800	Weak transcription	Brain Hippocampus Middle	brain
45	chr12:50083800-50088000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr12:50083800-50090600	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr12:50083800-50090800	Weak transcription	Brain Substantia Nigra	brain
48	chr12:50083800-50092400	Weak transcription	Duodenum Mucosa	Duodenum
49	chr12:50084000-50086200	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr12:50084000-50086400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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