Variant report

Variant	rs11800062
Chromosome Location	chr1:227348126-227348127
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 174 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:165)

rs_ID	r²[population]
rs1015815	0.80[AMR][1000 genomes]
rs10495258	0.93[EUR][1000 genomes]
rs10495263	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs10495266	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10495269	0.93[EUR][1000 genomes]
rs10495270	0.93[EUR][1000 genomes]
rs10916109	0.83[EUR][1000 genomes]
rs10916114	0.81[EUR][1000 genomes]
rs11799413	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11801443	0.92[EUR][1000 genomes]
rs11801994	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11802395	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11803590	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11803761	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11803959	0.92[EUR][1000 genomes]
rs11805298	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11806820	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11806937	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11808186	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11808928	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11809998	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11810328	0.81[EUR][1000 genomes]
rs12401556	0.91[EUR][1000 genomes]
rs12401963	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12402456	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12403195	0.93[EUR][1000 genomes]
rs12403391	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12403650	0.82[EUR][1000 genomes]
rs12403833	0.91[CEU][hapmap];0.93[EUR][1000 genomes]
rs12403986	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12404494	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12404627	0.93[EUR][1000 genomes]
rs12405122	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12405686	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12405707	0.91[EUR][1000 genomes]
rs12405723	0.86[EUR][1000 genomes]
rs12405878	1.00[CEU][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12407061	0.93[EUR][1000 genomes]
rs12407545	0.93[EUR][1000 genomes]
rs12408437	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12408913	0.82[EUR][1000 genomes]
rs12409816	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12410327	1.00[CEU][hapmap]
rs12410337	1.00[CEU][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12410460	1.00[CEU][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12411017	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1320493	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1464077	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1513600	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1513602	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1513603	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1546557	0.81[EUR][1000 genomes]
rs1606549	0.81[EUR][1000 genomes]
rs16846855	1.00[CEU][hapmap];0.81[YRI][hapmap];0.93[EUR][1000 genomes]
rs16846874	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16846877	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16846908	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16846910	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16846911	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16846972	1.00[CEU][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16846985	1.00[CEU][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16847014	1.00[CEU][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16847035	1.00[CEU][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16847098	1.00[CEU][hapmap];0.80[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16847107	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs16847492	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16847634	1.00[CEU][hapmap]
rs17605533	0.93[EUR][1000 genomes]
rs17613166	0.82[EUR][1000 genomes]
rs17851754	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1877622	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1888831	1.00[CEU][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2090009	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2150869	0.89[EUR][1000 genomes]
rs2150871	0.91[EUR][1000 genomes]
rs2150873	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2183837	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34400564	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34953255	0.93[EUR][1000 genomes]
rs41270149	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs41303115	0.91[EUR][1000 genomes]
rs4282782	0.81[EUR][1000 genomes]
rs4300186	1.00[CEU][hapmap]
rs4434814	0.81[EUR][1000 genomes]
rs4518864	0.81[EUR][1000 genomes]
rs4551563	0.93[EUR][1000 genomes]
rs55685166	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55805110	0.81[EUR][1000 genomes]
rs55865118	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55946024	0.82[EUR][1000 genomes]
rs56834719	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57276421	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs57513303	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57758974	0.81[EUR][1000 genomes]
rs58489467	0.83[EUR][1000 genomes]
rs58532064	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59116340	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59121440	0.81[EUR][1000 genomes]
rs59859849	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60068245	0.81[EUR][1000 genomes]
rs60079575	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60235610	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60291100	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60641481	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60866629	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60958272	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs60979561	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61081394	0.81[EUR][1000 genomes]
rs61522132	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6659506	0.81[EUR][1000 genomes]
rs6675383	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6696791	0.94[EUR][1000 genomes]
rs6696794	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6701743	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73086746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73086752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73086775	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73088658	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73089725	0.93[EUR][1000 genomes]
rs73089747	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73089755	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73089760	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73089765	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73089770	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73090612	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73091738	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73091740	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73091742	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73091755	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73091759	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73091761	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73091774	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73093463	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73093495	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73094351	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73094393	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73094400	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73096317	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73096350	0.83[EUR][1000 genomes]
rs73096353	0.83[EUR][1000 genomes]
rs73096358	0.81[EUR][1000 genomes]
rs73099023	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73099026	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73100804	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73100814	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73100852	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73102915	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73102920	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73102930	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73102936	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7413768	0.95[EUR][1000 genomes]
rs74140153	0.81[EUR][1000 genomes]
rs74140276	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs74143321	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7515739	0.81[EUR][1000 genomes]
rs7519099	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7526283	1.00[CEU][hapmap]
rs7534286	0.86[EUR][1000 genomes]
rs7535010	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7539037	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7539750	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7542505	1.00[CEU][hapmap]
rs7544923	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7545775	0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7551556	1.00[CEU][hapmap];0.81[EUR][1000 genomes]

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	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
4	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
5	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
6	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
7	nsv549270	chr1:227290139-227361072	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	esv2830098	chr1:227295716-227422234	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	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

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227259400-227349000	Weak transcription	Colonic Mucosa	Colon
2	chr1:227287400-227360800	Weak transcription	Psoas Muscle	Psoas
3	chr1:227288400-227398000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:227298600-227351800	Weak transcription	Hela-S3	cervix
5	chr1:227300000-227379800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:227316600-227352200	Weak transcription	Gastric	stomach
7	chr1:227317000-227374200	Weak transcription	HepG2	liver
8	chr1:227324200-227348400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:227326600-227355200	Weak transcription	Small Intestine	intestine
10	chr1:227327200-227348200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr1:227327200-227348200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr1:227328000-227354400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:227328400-227350000	Weak transcription	Fetal Brain Male	brain
14	chr1:227328600-227351600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr1:227328800-227354200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr1:227329600-227358400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:227329600-227380000	Weak transcription	Aorta	Aorta
18	chr1:227329800-227348400	Weak transcription	Fetal Brain Female	brain
19	chr1:227331600-227355000	Weak transcription	Brain Anterior Caudate	brain
20	chr1:227331600-227358400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr1:227332800-227350000	Weak transcription	HMEC	breast
22	chr1:227332800-227350200	Weak transcription	Lung	lung
23	chr1:227332800-227354600	Weak transcription	Ovary	ovary
24	chr1:227333000-227349400	Weak transcription	Placenta	Placenta
25	chr1:227333200-227354800	Weak transcription	Stomach Smooth Muscle	stomach
26	chr1:227333400-227354000	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr1:227333400-227354400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr1:227333400-227358400	Weak transcription	Osteobl	bone
29	chr1:227333400-227359000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr1:227333400-227381000	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr1:227333400-227405600	Weak transcription	Adipose Nuclei	Adipose
32	chr1:227334800-227371800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:227339600-227354000	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr1:227343200-227350600	Weak transcription	Stomach Mucosa	stomach
35	chr1:227343200-227352400	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr1:227343200-227400400	Weak transcription	A549	lung
37	chr1:227343600-227358400	Weak transcription	Colon Smooth Muscle	Colon
38	chr1:227344600-227348200	Strong transcription	HSMM	muscle
39	chr1:227345600-227348200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:227345800-227348200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:227346000-227348200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:227346000-227348200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:227346000-227348200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr1:227346200-227348200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:227346200-227348200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr1:227346200-227348200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:227346200-227348200	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr1:227346200-227348200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:227346200-227348200	Strong transcription	Fetal Intestine Large	intestine
50	chr1:227346200-227348200	Strong transcription	HUVEC	blood vessel

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