Variant report

Variant	rs12403986
Chromosome Location	chr1:227430742-227430743
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 124 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs1015815	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1015816	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10495263	1.00[CEU][hapmap]
rs10495266	0.80[AMR][1000 genomes]
rs10916109	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10916114	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11799413	1.00[CEU][hapmap];0.91[YRI][hapmap]
rs11800062	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11801994	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11803590	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11803761	1.00[CEU][hapmap];0.85[YRI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11805298	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11806511	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11806937	1.00[CEU][hapmap];0.83[YRI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11807094	0.90[YRI][hapmap]
rs11808928	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11808962	0.90[YRI][hapmap]
rs11810328	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11811358	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12402456	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12403650	0.95[EUR][1000 genomes]
rs12403833	0.87[CEU][hapmap]
rs12405363	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12405878	1.00[CEU][hapmap];0.95[YRI][hapmap]
rs12408913	0.95[EUR][1000 genomes]
rs12410327	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs12410337	1.00[CEU][hapmap];0.95[YRI][hapmap]
rs12410460	1.00[CEU][hapmap];0.95[YRI][hapmap]
rs12741049	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1464076	0.94[EUR][1000 genomes]
rs1464077	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1513602	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1513603	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1546557	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1606549	0.96[EUR][1000 genomes]
rs16846908	0.80[AMR][1000 genomes]
rs16846910	0.80[AMR][1000 genomes]
rs16846911	0.80[AMR][1000 genomes]
rs16846972	1.00[CEU][hapmap];0.95[YRI][hapmap]
rs16846985	1.00[CEU][hapmap];0.95[YRI][hapmap]
rs16847014	1.00[CEU][hapmap];0.95[YRI][hapmap]
rs16847035	1.00[CEU][hapmap];0.95[YRI][hapmap]
rs16847098	1.00[CEU][hapmap];0.95[YRI][hapmap]
rs16847107	1.00[CEU][hapmap];0.95[YRI][hapmap]
rs16847492	1.00[CEU][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16847634	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17613166	0.95[EUR][1000 genomes]
rs1877622	1.00[CEU][hapmap];0.83[YRI][hapmap]
rs1888831	1.00[CEU][hapmap];0.95[YRI][hapmap]
rs2150873	0.80[AMR][1000 genomes]
rs2183837	0.80[AMR][1000 genomes]
rs34263105	0.94[EUR][1000 genomes]
rs34400564	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs41270149	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4255349	0.93[EUR][1000 genomes]
rs4282782	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4300186	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4354510	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4434814	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4437846	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4518864	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4543764	0.87[EUR][1000 genomes]
rs55805110	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55865118	0.80[AMR][1000 genomes]
rs55882852	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55946024	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57276421	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57758974	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58489467	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs59116340	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59121440	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59859849	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60068245	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60235610	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60742095	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60866629	0.80[AMR][1000 genomes]
rs60958272	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs60979561	0.80[AMR][1000 genomes]
rs61081394	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61522132	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6659506	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6668367	0.92[EUR][1000 genomes]
rs6696794	0.80[AMR][1000 genomes]
rs73086746	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73086752	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73086775	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73088658	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73090612	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73091740	0.80[AMR][1000 genomes]
rs73091742	0.80[AMR][1000 genomes]
rs73091759	0.80[AMR][1000 genomes]
rs73091761	0.80[AMR][1000 genomes]
rs73091774	0.80[AMR][1000 genomes]
rs73094338	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs73094351	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73094393	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73094400	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73096317	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73096350	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73096353	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73096358	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73096374	0.95[EUR][1000 genomes]
rs73098390	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73098398	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73102307	0.90[EUR][1000 genomes]
rs74140145	0.81[EUR][1000 genomes]
rs74140153	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs74143321	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7515739	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7519099	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7526283	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7534286	0.91[EUR][1000 genomes]
rs7535010	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs7539037	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7539750	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7542505	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7544923	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7545775	0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7551556	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227386200-227433400	Weak transcription	Fetal Stomach	stomach
2	chr1:227407200-227432400	Weak transcription	Right Ventricle	heart
3	chr1:227411800-227431400	Weak transcription	Fetal Intestine Small	intestine
4	chr1:227414000-227433200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr1:227414000-227459200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:227414200-227433400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr1:227414200-227453800	Weak transcription	HSMM	muscle
8	chr1:227414400-227432400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr1:227414400-227432600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr1:227415800-227456800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr1:227416200-227431800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:227420800-227434600	Weak transcription	Spleen	Spleen
13	chr1:227422000-227430800	Weak transcription	Ovary	ovary
14	chr1:227422600-227430800	Weak transcription	Gastric	stomach
15	chr1:227423000-227432400	Weak transcription	Small Intestine	intestine
16	chr1:227423600-227430800	Weak transcription	Colon Smooth Muscle	Colon
17	chr1:227423600-227431400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr1:227423600-227432000	Weak transcription	Brain Substantia Nigra	brain
19	chr1:227424000-227430800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:227424600-227430800	Weak transcription	NHEK	skin
21	chr1:227424800-227430800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:227424800-227432600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:227424800-227440800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:227425200-227432400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:227425400-227430800	Weak transcription	HUVEC	blood vessel
26	chr1:227425400-227445200	Weak transcription	Osteobl	bone
27	chr1:227426000-227432400	Weak transcription	Left Ventricle	heart
28	chr1:227427000-227432400	Weak transcription	Brain Angular Gyrus	brain
29	chr1:227427200-227430800	Weak transcription	Brain Hippocampus Middle	brain
30	chr1:227427200-227433200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:227427600-227432200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:227428400-227431400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr1:227428400-227432600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:227429000-227431400	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr1:227429000-227432600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr1:227429200-227431400	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr1:227429600-227431600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr1:227429800-227431400	Enhancers	Pancreatic Islets	Pancreatic Islet
39	chr1:227430400-227430800	Weak transcription	Aorta	Aorta
40	chr1:227430400-227430800	Enhancers	HepG2	liver
41	chr1:227430400-227431000	Flanking Active TSS	Liver	Liver
42	chr1:227430400-227431000	Enhancers	A549	lung
43	chr1:227430400-227432600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr1:227430600-227430800	Enhancers	Psoas Muscle	Psoas
45	chr1:227430600-227431000	Enhancers	Right Atrium	heart
46	chr1:227430600-227431200	Weak transcription	Fetal Kidney	kidney
47	chr1:227430600-227431200	Enhancers	Stomach Mucosa	stomach
48	chr1:227430600-227431400	Enhancers	Adipose Nuclei	Adipose
49	chr1:227430600-227431600	Enhancers	Muscle Satellite Cultured Cells	--
50	chr1:227430600-227432800	Enhancers	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links