Variant report

Variant	rs7515739
Chromosome Location	chr1:227455092-227455093
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr1:227454805-227455472	SK-N-SH	brain:	n/a	chr1:227455042-227455049 chr1:227455042-227455049 chr1:227455192-227455204 chr1:227455191-227455198 chr1:227455042-227455049
2	GATA3	chr1:227454758-227455446	SK-N-SH	brain:	n/a	chr1:227455042-227455049 chr1:227455042-227455049 chr1:227455192-227455204 chr1:227455191-227455198 chr1:227455042-227455049

No.	Distal block	Cell Line	Cell type
1	chr1:227441285..227444497-chr1:227452902..227455834,3	K562	blood:
2	chr1:227454247..227456630-chr1:227461574..227463571,2	K562	blood:
3	chr1:227453649..227455713-chr1:227502343..227504921,2	K562	blood:

Variant related genes	Relation type
ENSG00000236636	TF binding region
ENSG00000143776	Chromatin interaction

Extended variants
information (count: 131 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs1015815	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1015816	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10916109	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10916114	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11799413	0.83[AMR][1000 genomes]
rs11800062	0.81[EUR][1000 genomes]
rs11801994	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11803590	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11803761	0.92[EUR][1000 genomes]
rs11805298	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11806511	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11806820	0.83[AMR][1000 genomes]
rs11806937	0.92[EUR][1000 genomes]
rs11808928	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11809998	0.83[AMR][1000 genomes]
rs11810328	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11811358	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12402456	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12403391	0.83[AMR][1000 genomes]
rs12403650	0.94[EUR][1000 genomes]
rs12403986	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12404494	0.83[AMR][1000 genomes]
rs12405122	0.83[AMR][1000 genomes]
rs12405363	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12405878	0.83[AMR][1000 genomes]
rs12408437	0.83[AMR][1000 genomes]
rs12408913	0.94[EUR][1000 genomes]
rs12409816	0.81[AMR][1000 genomes]
rs12410327	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12410337	0.83[AMR][1000 genomes]
rs12410460	0.83[AMR][1000 genomes]
rs12411017	0.83[AMR][1000 genomes]
rs12741049	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1464076	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1464077	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1513600	0.83[AMR][1000 genomes]
rs1513602	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1513603	0.92[EUR][1000 genomes]
rs1546557	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1606549	0.80[AMR][1000 genomes];0.95[EUR][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	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16847634	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17613166	0.94[EUR][1000 genomes]
rs1888831	0.83[AMR][1000 genomes]
rs2090009	0.83[AMR][1000 genomes]
rs34263105	0.98[EUR][1000 genomes]
rs34400564	0.92[EUR][1000 genomes]
rs41270149	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4255349	0.96[EUR][1000 genomes]
rs4282782	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4300186	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4354510	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4434814	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4437846	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4518864	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4543764	0.91[EUR][1000 genomes]
rs55805110	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55882852	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55946024	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56389454	0.81[AFR][1000 genomes]
rs56834719	0.83[AMR][1000 genomes]
rs57276421	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57513303	0.83[AMR][1000 genomes]
rs57758974	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58489467	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58912997	0.83[AFR][1000 genomes]
rs59116340	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59121440	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59859849	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60068245	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60079575	0.81[AMR][1000 genomes]
rs60235610	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60291100	0.83[AMR][1000 genomes]
rs60641481	0.83[AMR][1000 genomes]
rs60742095	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs60958272	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61081394	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61522132	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6659506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6668367	0.95[EUR][1000 genomes]
rs6675383	0.83[AMR][1000 genomes]
rs6701743	0.83[AMR][1000 genomes]
rs73086746	0.81[EUR][1000 genomes]
rs73086752	0.81[EUR][1000 genomes]
rs73086775	0.81[EUR][1000 genomes]
rs73088658	0.92[EUR][1000 genomes]
rs73090612	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73093463	0.83[AMR][1000 genomes]
rs73093495	0.83[AMR][1000 genomes]
rs73094351	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73094393	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73094400	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73096317	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73096350	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73096353	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73096358	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73096374	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73098390	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73098398	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[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]
rs73102307	0.93[EUR][1000 genomes]
rs73102915	0.83[AMR][1000 genomes]
rs73102920	0.83[AMR][1000 genomes]
rs73102930	0.83[AMR][1000 genomes]
rs73102936	0.83[AMR][1000 genomes]
rs74140153	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74140155	0.83[AFR][1000 genomes]
rs7519099	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7526283	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7534286	0.90[EUR][1000 genomes]
rs7535010	0.90[EUR][1000 genomes]
rs7539037	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7539750	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7542505	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7544923	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7545775	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7551556	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227414000-227459200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:227415800-227456800	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr1:227431600-227486200	Weak transcription	NHDF-Ad	bronchial
4	chr1:227432000-227459200	Weak transcription	Fetal Lung	lung
5	chr1:227432200-227455400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr1:227432800-227455600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr1:227433000-227469000	Weak transcription	Aorta	Aorta
8	chr1:227434200-227455400	Weak transcription	Left Ventricle	heart
9	chr1:227434200-227455400	Weak transcription	Right Ventricle	heart
10	chr1:227434200-227455800	Weak transcription	Adipose Nuclei	Adipose
11	chr1:227434600-227468800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:227434800-227458400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:227435000-227457000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr1:227440000-227456600	Weak transcription	HepG2	liver
15	chr1:227440200-227456800	Weak transcription	HUVEC	blood vessel
16	chr1:227443400-227474000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:227445800-227458400	Weak transcription	NHEK	skin
18	chr1:227447000-227456800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr1:227447200-227473600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:227448400-227456400	Weak transcription	Psoas Muscle	Psoas
21	chr1:227448600-227457200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr1:227449600-227473600	Weak transcription	NH-A	brain
23	chr1:227449800-227465200	Weak transcription	K562	blood
24	chr1:227452400-227456000	Enhancers	Brain Hippocampus Middle	brain
25	chr1:227452800-227463800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:227453000-227468600	Weak transcription	Lung	lung
27	chr1:227453600-227457200	Enhancers	Brain Substantia Nigra	brain
28	chr1:227454000-227455400	Enhancers	Pancreatic Islets	Pancreatic Islet
29	chr1:227454200-227455200	Weak transcription	Brain Anterior Caudate	brain
30	chr1:227454200-227455400	Weak transcription	Brain Angular Gyrus	brain
31	chr1:227454200-227470400	Weak transcription	Ovary	ovary
32	chr1:227454600-227455400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr1:227454600-227455600	Weak transcription	Colon Smooth Muscle	Colon
34	chr1:227454600-227455600	Weak transcription	Rectal Smooth Muscle	rectum
35	chr1:227454800-227455200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr1:227455000-227457200	Enhancers	Brain Inferior Temporal Lobe	brain

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