Variant report

Variant	rs12403391
Chromosome Location	chr1:227287627-227287628
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 168 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:159)

rs_ID	r²[population]
rs1015815	0.86[AMR][1000 genomes]
rs1015816	0.80[AMR][1000 genomes]
rs10495258	0.98[EUR][1000 genomes]
rs10495263	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs10495266	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10495269	0.98[EUR][1000 genomes]
rs10495270	0.98[EUR][1000 genomes]
rs10916109	0.83[AMR][1000 genomes]
rs10916114	0.81[AMR][1000 genomes]
rs11799413	1.00[CEU][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11800062	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11801443	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11802395	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11803761	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11803959	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11805298	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11806820	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11806937	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11807094	1.00[YRI][hapmap]
rs11808186	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11808962	1.00[YRI][hapmap]
rs11809998	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11810328	0.83[AMR][1000 genomes]
rs11811358	0.83[AMR][1000 genomes]
rs12401556	0.95[EUR][1000 genomes]
rs12401963	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12403195	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12403833	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs12404494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12404627	0.98[EUR][1000 genomes]
rs12405122	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12405686	1.00[CEU][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12405707	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12405723	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12405878	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12407061	0.98[EUR][1000 genomes]
rs12407545	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12408437	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12409816	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12410327	1.00[CEU][hapmap]
rs12410337	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12410460	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12411017	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1320493	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1464077	1.00[CEU][hapmap];0.95[YRI][hapmap];0.83[AMR][1000 genomes]
rs1513600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1513602	0.83[AMR][1000 genomes]
rs1513603	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1546557	0.83[AMR][1000 genomes]
rs16846855	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16846874	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16846877	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16846908	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16846910	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16846911	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16846972	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16846985	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16847014	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16847035	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16847098	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16847107	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs16847492	1.00[CEU][hapmap]
rs17605533	0.98[EUR][1000 genomes]
rs17851754	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1877622	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1888830	0.80[AFR][1000 genomes]
rs1888831	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2090009	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2150869	0.94[EUR][1000 genomes]
rs2150871	0.94[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2150873	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2183837	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34400564	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34953255	0.98[EUR][1000 genomes]
rs41303115	0.95[EUR][1000 genomes]
rs4282782	0.83[AMR][1000 genomes]
rs4354510	0.83[AMR][1000 genomes]
rs4434814	0.83[AMR][1000 genomes]
rs4437846	0.81[AMR][1000 genomes]
rs4518864	0.83[AMR][1000 genomes]
rs4551563	0.98[EUR][1000 genomes]
rs55685166	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55805110	0.83[AMR][1000 genomes]
rs55865118	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55946024	0.83[AMR][1000 genomes]
rs56834719	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57513303	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58489467	0.83[AMR][1000 genomes]
rs58532064	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59116340	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59121440	0.83[AMR][1000 genomes]
rs59859849	0.83[AMR][1000 genomes]
rs60068245	0.83[AMR][1000 genomes]
rs60079575	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60291100	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60641481	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60742095	0.83[AMR][1000 genomes]
rs60866629	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60979561	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61081394	0.83[AMR][1000 genomes]
rs61522132	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6659506	0.83[AMR][1000 genomes]
rs6675383	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6696791	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6696794	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6701743	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73086746	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73086752	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73086775	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73088658	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73089725	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73089746	0.81[AFR][1000 genomes]
rs73089747	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73089755	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73089760	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73089765	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73089770	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73090612	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73091738	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73091740	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73091742	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73091755	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73091757	0.81[AFR][1000 genomes]
rs73091759	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73091761	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73091766	0.81[AFR][1000 genomes]
rs73091774	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73093463	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73093467	0.80[AFR][1000 genomes]
rs73093495	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73096350	0.83[AMR][1000 genomes]
rs73096353	0.83[AMR][1000 genomes]
rs73096358	0.83[AMR][1000 genomes]
rs73096883	0.83[AFR][1000 genomes]
rs73099023	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73099026	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73100804	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73100813	0.81[AFR][1000 genomes]
rs73100814	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73100852	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73102915	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73102920	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73102930	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73102936	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7413768	0.95[EUR][1000 genomes]
rs74140153	0.83[AMR][1000 genomes]
rs74140276	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs74140278	0.81[AFR][1000 genomes]
rs74140289	0.83[AFR][1000 genomes]
rs74143321	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7515739	0.83[AMR][1000 genomes]
rs7526283	1.00[CEU][hapmap]
rs7534286	0.82[EUR][1000 genomes]
rs7535010	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7539037	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7539750	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7542505	1.00[CEU][hapmap]
rs7545775	0.94[YRI][hapmap]
rs7551556	1.00[CEU][hapmap];0.94[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv1011654	chr1:227196502-227308416	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv832792	chr1:227211378-227364992	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv873239	chr1:227222125-227361072	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv468227	chr1:227223736-227340790	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv549269	chr1:227223736-227340790	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv873240	chr1:227228946-227361072	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv873241	chr1:227242247-227361072	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227154400-227294200	Weak transcription	Hela-S3	cervix
2	chr1:227209200-227301600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:227214800-227329200	Weak transcription	Right Ventricle	heart
4	chr1:227220600-227288000	Weak transcription	Colon Smooth Muscle	Colon
5	chr1:227247400-227299800	Weak transcription	HMEC	breast
6	chr1:227251000-227300000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:227257600-227288000	Weak transcription	HSMMtube	muscle
8	chr1:227257800-227312200	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:227259400-227349000	Weak transcription	Colonic Mucosa	Colon
10	chr1:227260400-227287800	Weak transcription	NHEK	skin
11	chr1:227261400-227287800	Weak transcription	Osteobl	bone
12	chr1:227271800-227287800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:227271800-227288000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr1:227271800-227299600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:227272600-227294400	Weak transcription	Fetal Heart	heart
16	chr1:227272800-227295000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:227272800-227295000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr1:227272800-227331000	Weak transcription	Lung	lung
19	chr1:227273000-227312400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr1:227275800-227302600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr1:227277000-227288600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:227277200-227302600	Weak transcription	Brain Substantia Nigra	brain
23	chr1:227279200-227287800	Weak transcription	Aorta	Aorta
24	chr1:227279200-227287800	Weak transcription	Brain Anterior Caudate	brain
25	chr1:227279200-227287800	Weak transcription	Fetal Stomach	stomach
26	chr1:227279400-227288000	Weak transcription	NH-A	brain
27	chr1:227279800-227299000	Weak transcription	Placenta	Placenta
28	chr1:227280800-227298800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr1:227281800-227294400	Weak transcription	Fetal Kidney	kidney
30	chr1:227282400-227287800	Weak transcription	NHLF	lung
31	chr1:227282400-227288000	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr1:227282600-227318000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:227283000-227287800	Weak transcription	HepG2	liver
34	chr1:227283800-227288600	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr1:227284000-227288800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr1:227284400-227288600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr1:227284800-227288600	Strong transcription	Brain Hippocampus Middle	brain
38	chr1:227285000-227288600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:227285200-227288200	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr1:227285200-227288600	Strong transcription	Fetal Brain Female	brain
41	chr1:227285200-227288600	Strong transcription	Fetal Muscle Trunk	muscle
42	chr1:227285200-227288600	Strong transcription	Fetal Muscle Leg	muscle
43	chr1:227285200-227289000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr1:227285400-227288600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr1:227285400-227288600	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr1:227285400-227288800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:227285600-227287800	Weak transcription	Fetal Intestine Large	intestine
48	chr1:227285600-227288600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr1:227285600-227288600	Strong transcription	Left Ventricle	heart
50	chr1:227285600-227288800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links