Variant report

Variant	rs1513602
Chromosome Location	chr1:227392568-227392569
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	chr1:227383751..227387113-chr1:227389765..227393443,4	K562	blood:

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

rSNPs within LD-proxies of this variant (count:161)

rs_ID	r²[population]
rs1015815	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1015816	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10495266	0.89[AMR][1000 genomes]
rs10916109	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10916114	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11799413	0.83[AMR][1000 genomes]
rs11800062	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11801994	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11802395	0.83[AMR][1000 genomes]
rs11803590	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11803761	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11805298	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11806511	0.93[EUR][1000 genomes]
rs11806820	0.83[AMR][1000 genomes]
rs11806937	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11808186	0.83[AMR][1000 genomes]
rs11808928	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11809998	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11810328	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11811358	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12402456	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12403391	0.83[AMR][1000 genomes]
rs12403650	0.98[EUR][1000 genomes]
rs12403986	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12404494	0.83[AMR][1000 genomes]
rs12405122	0.83[AMR][1000 genomes]
rs12405363	0.94[EUR][1000 genomes]
rs12405878	0.83[AMR][1000 genomes]
rs12408437	0.83[AMR][1000 genomes]
rs12408913	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12409816	0.81[AMR][1000 genomes]
rs12410327	0.94[EUR][1000 genomes]
rs12410337	0.83[AMR][1000 genomes]
rs12410460	0.83[AMR][1000 genomes]
rs12411017	0.83[AMR][1000 genomes]
rs12741049	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1320493	0.86[AMR][1000 genomes]
rs1464076	0.94[EUR][1000 genomes]
rs1464077	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1513600	0.83[AMR][1000 genomes]
rs1513603	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1546557	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1606549	0.96[EUR][1000 genomes]
rs16846874	0.83[AMR][1000 genomes]
rs16846877	0.83[AMR][1000 genomes]
rs16846908	0.89[AMR][1000 genomes]
rs16846910	0.89[AMR][1000 genomes]
rs16846911	0.89[AMR][1000 genomes]
rs16846972	0.83[AMR][1000 genomes]
rs16846985	0.83[AMR][1000 genomes]
rs16847014	0.83[AMR][1000 genomes]
rs16847035	0.83[AMR][1000 genomes]
rs16847098	0.83[AMR][1000 genomes]
rs16847492	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16847634	0.94[EUR][1000 genomes]
rs17613166	0.98[EUR][1000 genomes]
rs17851754	0.83[AMR][1000 genomes]
rs1877622	0.83[AMR][1000 genomes]
rs1888831	0.83[AMR][1000 genomes]
rs2090009	0.83[AMR][1000 genomes]
rs2150873	0.89[AMR][1000 genomes]
rs2183837	0.89[AMR][1000 genomes]
rs34263105	0.94[EUR][1000 genomes]
rs34400564	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs41270149	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4255349	0.93[EUR][1000 genomes]
rs4282782	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4300186	0.94[EUR][1000 genomes]
rs4354510	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4434814	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4437846	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4518864	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4543764	0.87[EUR][1000 genomes]
rs55685166	0.83[AMR][1000 genomes]
rs55805110	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55865118	0.89[AMR][1000 genomes]
rs55882852	0.95[EUR][1000 genomes]
rs55946024	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56834719	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs57276421	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57513303	0.83[AMR][1000 genomes]
rs57752854	0.81[AFR][1000 genomes]
rs57758974	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58489467	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58532064	0.83[AMR][1000 genomes]
rs59116340	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59121440	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59859849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60068245	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60079575	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs60235610	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60291100	0.83[AMR][1000 genomes]
rs60641481	0.83[AMR][1000 genomes]
rs60742095	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60866629	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs60958272	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs60979561	0.89[AMR][1000 genomes]
rs61081394	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61522132	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6659506	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6668367	0.92[EUR][1000 genomes]
rs6675383	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6696794	0.89[AMR][1000 genomes]
rs6701743	0.83[AMR][1000 genomes]
rs73086746	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73086752	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73086775	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73088658	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73089747	0.83[AMR][1000 genomes]
rs73089755	0.83[AMR][1000 genomes]
rs73089760	0.83[AMR][1000 genomes]
rs73089765	0.83[AMR][1000 genomes]
rs73089770	0.83[AMR][1000 genomes]
rs73090612	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73091738	0.83[AMR][1000 genomes]
rs73091740	0.89[AMR][1000 genomes]
rs73091742	0.89[AMR][1000 genomes]
rs73091755	0.86[AMR][1000 genomes]
rs73091759	0.89[AMR][1000 genomes]
rs73091761	0.89[AMR][1000 genomes]
rs73091774	0.89[AMR][1000 genomes]
rs73092602	0.81[AFR][1000 genomes]
rs73093463	0.83[AMR][1000 genomes]
rs73093495	0.83[AMR][1000 genomes]
rs73094331	0.81[AFR][1000 genomes]
rs73094338	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs73094351	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73094393	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73094400	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73096317	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73096350	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73096353	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73096358	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73096374	0.95[EUR][1000 genomes]
rs73098390	0.94[EUR][1000 genomes]
rs73098398	0.94[EUR][1000 genomes]
rs73099023	0.83[AMR][1000 genomes]
rs73099026	0.83[AMR][1000 genomes]
rs73100804	0.83[AMR][1000 genomes]
rs73100814	0.83[AMR][1000 genomes]
rs73100852	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73102307	0.90[EUR][1000 genomes]
rs73102915	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73102920	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73102930	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73102936	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs74140145	0.81[EUR][1000 genomes]
rs74140153	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs74140276	0.83[AMR][1000 genomes]
rs74143321	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7515739	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7519099	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7526283	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7534286	0.93[EUR][1000 genomes]
rs7535010	0.93[EUR][1000 genomes]
rs7539037	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7539750	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7542505	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7544923	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7545775	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7551556	0.89[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	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
4	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
5	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

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227288400-227398000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:227333400-227405600	Weak transcription	Adipose Nuclei	Adipose
3	chr1:227343200-227400400	Weak transcription	A549	lung
4	chr1:227346800-227403800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr1:227346800-227405800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr1:227346800-227406800	Weak transcription	Fetal Kidney	kidney
7	chr1:227348200-227398000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr1:227348200-227398400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr1:227348200-227401600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:227348200-227408400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:227348200-227412200	Weak transcription	Fetal Muscle Leg	muscle
12	chr1:227360800-227401200	Weak transcription	Hela-S3	cervix
13	chr1:227365800-227399400	Weak transcription	Fetal Intestine Large	intestine
14	chr1:227370000-227413600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr1:227373400-227397800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:227374400-227401600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr1:227374600-227401600	Weak transcription	Left Ventricle	heart
18	chr1:227375600-227410800	Weak transcription	HepG2	liver
19	chr1:227376600-227412600	Weak transcription	Fetal Lung	lung
20	chr1:227378400-227401000	Weak transcription	Placenta	Placenta
21	chr1:227379000-227398000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:227379000-227398000	Weak transcription	Liver	Liver
23	chr1:227379600-227399200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:227380200-227402200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr1:227380200-227405200	Weak transcription	Gastric	stomach
26	chr1:227380200-227421800	Weak transcription	Ovary	ovary
27	chr1:227380400-227398000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr1:227380400-227398000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:227380400-227400000	Weak transcription	HSMMtube	muscle
30	chr1:227380400-227400000	Weak transcription	NHEK	skin
31	chr1:227380400-227404000	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr1:227380400-227406800	Weak transcription	NHDF-Ad	bronchial
33	chr1:227380800-227398400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:227381600-227398000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:227381600-227406600	Weak transcription	Duodenum Mucosa	Duodenum
36	chr1:227381800-227397800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:227382000-227398000	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr1:227382000-227414000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr1:227382600-227398000	Weak transcription	K562	blood
40	chr1:227382600-227398400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:227383600-227421800	Weak transcription	Stomach Smooth Muscle	stomach
42	chr1:227385000-227400000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr1:227386000-227397800	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr1:227386200-227398000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:227386200-227433400	Weak transcription	Fetal Stomach	stomach
46	chr1:227386400-227413800	Weak transcription	Brain Anterior Caudate	brain
47	chr1:227386800-227399400	Weak transcription	HUVEC	blood vessel
48	chr1:227386800-227406600	Weak transcription	Fetal Intestine Small	intestine
49	chr1:227387000-227413600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:227387400-227397800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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