Variant report

Variant	rs2090009
Chromosome Location	chr1:227313362-227313363
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	chr1:227312511..227315121-chr1:227315946..227317817,2	K562	blood:

Extended variants
information (count: 166 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:156)

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	0.94[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];0.96[YRI][hapmap];0.94[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	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11802395	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11803761	1.00[CEU][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11803959	0.92[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	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11806937	1.00[CEU][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11807094	0.96[YRI][hapmap]
rs11808186	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11808962	0.95[YRI][hapmap]
rs11809998	0.92[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];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12403195	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12403391	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12403833	0.91[CEU][hapmap];0.98[EUR][1000 genomes]
rs12404494	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12404627	0.98[EUR][1000 genomes]
rs12405122	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12405686	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12405707	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12405723	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12405878	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12407061	0.98[EUR][1000 genomes]
rs12407545	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12408437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12409816	0.96[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];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12410460	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12411017	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1320493	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1464077	1.00[CEU][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes]
rs1513600	0.98[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];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16846874	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16846877	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16846908	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16846910	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16846911	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16846972	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16846985	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16847014	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16847035	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16847098	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[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]
rs16847634	1.00[CEU][hapmap];0.96[YRI][hapmap]
rs17605533	0.98[EUR][1000 genomes]
rs17851754	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1877622	1.00[CEU][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1888831	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2150869	0.94[EUR][1000 genomes]
rs2150871	0.92[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2150873	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2183837	0.94[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]
rs4300186	1.00[CEU][hapmap];0.95[YRI][hapmap]
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	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55805110	0.83[AMR][1000 genomes]
rs55865118	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55946024	0.83[AMR][1000 genomes]
rs56834719	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57513303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57758974	0.83[AMR][1000 genomes]
rs58489467	0.83[AMR][1000 genomes]
rs58532064	0.94[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	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60291100	1.00[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	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60979561	0.94[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	0.92[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	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6701743	0.98[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	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73089747	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73089755	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73089760	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73089765	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73089770	0.94[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	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73091740	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73091742	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73091755	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73091759	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73091761	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73091774	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73093463	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73093495	0.96[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	0.81[AFR][1000 genomes]
rs73099023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73099026	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73100804	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73100813	0.83[AFR][1000 genomes]
rs73100814	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73100852	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73102915	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73102920	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73102930	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73102936	0.92[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	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs74140289	0.81[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	0.95[YRI][hapmap]
rs7551556	1.00[CEU][hapmap];0.95[YRI][hapmap];0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
6	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
7	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
8	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
9	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
10	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227214800-227329200	Weak transcription	Right Ventricle	heart
2	chr1:227259400-227349000	Weak transcription	Colonic Mucosa	Colon
3	chr1:227272800-227331000	Weak transcription	Lung	lung
4	chr1:227282600-227318000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:227285600-227313800	Weak transcription	Gastric	stomach
6	chr1:227286400-227328200	Weak transcription	Brain Germinal Matrix	brain
7	chr1:227287400-227360800	Weak transcription	Psoas Muscle	Psoas
8	chr1:227288000-227326400	Weak transcription	A549	lung
9	chr1:227288200-227332400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:227288400-227343000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:227288400-227398000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:227288600-227316000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr1:227288600-227328200	Weak transcription	Fetal Stomach	stomach
14	chr1:227288600-227332400	Weak transcription	NHLF	lung
15	chr1:227288600-227333600	Weak transcription	Esophagus	oesophagus
16	chr1:227288800-227317200	Weak transcription	NHEK	skin
17	chr1:227288800-227330000	Weak transcription	NHDF-Ad	bronchial
18	chr1:227295200-227316000	Weak transcription	Fetal Kidney	kidney
19	chr1:227295200-227346400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:227295400-227313800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr1:227296400-227326200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:227296600-227316400	Weak transcription	HSMMtube	muscle
23	chr1:227296600-227326200	Weak transcription	Fetal Lung	lung
24	chr1:227298600-227351800	Weak transcription	Hela-S3	cervix
25	chr1:227299200-227318800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr1:227299800-227313800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr1:227299800-227319600	Weak transcription	Fetal Intestine Large	intestine
28	chr1:227299800-227332600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr1:227300000-227315800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr1:227300000-227316200	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr1:227300000-227316400	Weak transcription	Osteobl	bone
32	chr1:227300000-227321800	Weak transcription	Colon Smooth Muscle	Colon
33	chr1:227300000-227325800	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr1:227300000-227326400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr1:227300000-227328600	Weak transcription	Fetal Brain Female	brain
36	chr1:227300000-227329200	Weak transcription	Aorta	Aorta
37	chr1:227300000-227333800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr1:227300000-227379800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:227300200-227315200	Weak transcription	Adipose Nuclei	Adipose
40	chr1:227300200-227315600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:227300200-227315600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:227300200-227316200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:227300200-227316200	Weak transcription	HepG2	liver
44	chr1:227300200-227322000	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr1:227300200-227322600	Weak transcription	Ovary	ovary
46	chr1:227300200-227326200	Weak transcription	Liver	Liver
47	chr1:227300200-227326400	Weak transcription	Stomach Smooth Muscle	stomach
48	chr1:227300200-227334400	Weak transcription	Stomach Mucosa	stomach
49	chr1:227300600-227313800	Weak transcription	Left Ventricle	heart
50	chr1:227300600-227315600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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