Variant report

Variant	rs1859571
Chromosome Location	chr7:50852020-50852021
allele	G/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	POLR2A	chr7:50850323-50853302	A549	lung:	n/a	n/a
2	POLR2A	chr7:50852016-50852201	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:50826494..50829462-chr7:50851162..50853620,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IKZF1-9	chr7:50850753-50853616	NONHSAT120577

Variant related genes	Relation type
GRB10	TF binding region

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1014384	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1015573	0.81[ASN][1000 genomes]
rs1019000	0.83[AMR][1000 genomes]
rs10226937	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10231012	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10235345	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10239268	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1024531	0.86[AMR][1000 genomes]
rs10248029	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10258458	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10264904	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10268643	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10273302	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10276986	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10281065	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10464765	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10464766	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10464790	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10486761	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11238310	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11238311	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11238313	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11238315	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11238325	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11238326	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11238337	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11238339	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11974751	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11978750	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11983539	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12671577	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12674028	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12718925	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12718926	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12718927	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12718929	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12718930	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13232029	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2051895	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2051896	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2074719	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2074720	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2074721	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2074722	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2158670	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2286152	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2286154	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2329554	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2876846	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3801000	0.86[AMR][1000 genomes]
rs6593164	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6593173	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6593174	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6593180	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6593200	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6943901	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6945597	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6946194	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6951356	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6957007	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6958750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6960912	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6963498	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6966774	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6971834	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6979369	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs734422	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs757773	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs757774	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs757777	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs757778	0.94[AFR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7785908	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7785914	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7786917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7788511	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7791286	0.81[AFR][1000 genomes]
rs7802338	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7803278	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7809623	0.81[AMR][1000 genomes]
rs886700	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016665	chr7:50452552-51404524	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv824091	chr7:50828682-50885984	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv538835	chr7:50839656-50867735	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv824092	chr7:50846084-50865531	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50848000-50855200	Weak transcription	Hela-S3	cervix
2	chr7:50850800-50855400	Enhancers	Liver	Liver
3	chr7:50850800-50858600	Weak transcription	Aorta	Aorta
4	chr7:50851000-50852200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr7:50851000-50852200	Enhancers	Adipose Nuclei	Adipose
6	chr7:50851000-50852400	Enhancers	Duodenum Mucosa	Duodenum
7	chr7:50851000-50853000	Enhancers	Pancreas	Pancrea
8	chr7:50851000-50853400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr7:50851000-50853400	Enhancers	Gastric	stomach
10	chr7:50851000-50853400	Enhancers	Left Ventricle	heart
11	chr7:50851000-50853400	Enhancers	Lung	lung
12	chr7:50851000-50853400	Enhancers	Ovary	ovary
13	chr7:50851000-50853400	Enhancers	Right Ventricle	heart
14	chr7:50851000-50853400	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr7:50851000-50854000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr7:50851000-50854400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr7:50851000-50856000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr7:50851000-50859000	Weak transcription	NHLF	lung
19	chr7:50851200-50852200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
20	chr7:50851200-50852200	Enhancers	NH-A	brain
21	chr7:50851200-50852400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr7:50851200-50852400	Enhancers	Brain Hippocampus Middle	brain
23	chr7:50851200-50852400	Enhancers	Colon Smooth Muscle	Colon
24	chr7:50851200-50852600	Enhancers	H1 Cell Line	embryonic stem cell
25	chr7:50851200-50852600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr7:50851200-50853400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr7:50851200-50853400	Genic enhancers	Spleen	Spleen
28	chr7:50851200-50854800	Weak transcription	Esophagus	oesophagus
29	chr7:50851200-50855200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr7:50851200-50855600	Weak transcription	Primary T cells from cord blood	blood
31	chr7:50851200-50857000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr7:50851400-50852200	Enhancers	Brain Cingulate Gyrus	brain
33	chr7:50851400-50852400	Enhancers	HUVEC	blood vessel
34	chr7:50851400-50852600	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr7:50851400-50852600	Enhancers	HSMM	muscle
36	chr7:50851400-50853200	Enhancers	Brain Substantia Nigra	brain
37	chr7:50851400-50853400	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr7:50851400-50855200	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr7:50851400-50857800	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr7:50851400-50858200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr7:50851600-50852600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr7:50851600-50852600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr7:50851600-50852600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
44	chr7:50851600-50852600	Genic enhancers	K562	blood
45	chr7:50851600-50853000	Enhancers	Fetal Brain Male	brain
46	chr7:50851600-50854800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr7:50851600-50856000	Weak transcription	A549	lung
48	chr7:50851600-50857600	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr7:50851600-50857600	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr7:50851600-50857800	Weak transcription	Rectal Smooth Muscle	rectum

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