Variant report

Variant	rs58649883
Chromosome Location	chr1:224554281-224554282
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	chr1:224552027..224554315-chr1:224555150..224556880,2	K562	blood:
2	chr1:224543261..224548633-chr1:224550034..224557593,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143771	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10495218	0.82[AFR][1000 genomes]
rs10495221	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11801211	1.00[EUR][1000 genomes]
rs11802182	1.00[EUR][1000 genomes]
rs11807149	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11809688	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11809710	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11810160	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11811935	1.00[EUR][1000 genomes]
rs11812007	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12239466	1.00[EUR][1000 genomes]
rs1401319	1.00[EUR][1000 genomes]
rs1499284	1.00[EUR][1000 genomes]
rs16846190	1.00[EUR][1000 genomes]
rs16846212	1.00[EUR][1000 genomes]
rs16846293	1.00[EUR][1000 genomes]
rs16846494	1.00[EUR][1000 genomes]
rs16847675	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16847784	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16847858	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16847870	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16847871	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16849419	1.00[EUR][1000 genomes]
rs16849547	1.00[EUR][1000 genomes]
rs1857042	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2068945	1.00[EUR][1000 genomes]
rs2794805	1.00[EUR][1000 genomes]
rs4653586	1.00[EUR][1000 genomes]
rs55712053	1.00[EUR][1000 genomes]
rs57102803	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57469223	1.00[EUR][1000 genomes]
rs57719044	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57967341	1.00[EUR][1000 genomes]
rs58304668	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58788859	1.00[EUR][1000 genomes]
rs58814229	1.00[EUR][1000 genomes]
rs58954846	1.00[EUR][1000 genomes]
rs59034185	1.00[EUR][1000 genomes]
rs59561838	1.00[EUR][1000 genomes]
rs59577766	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59710928	1.00[EUR][1000 genomes]
rs59734390	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs60063902	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs60349703	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60627429	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60715845	1.00[EUR][1000 genomes]
rs60831135	1.00[EUR][1000 genomes]
rs61000820	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61155217	1.00[EUR][1000 genomes]
rs61278437	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6426167	1.00[EUR][1000 genomes]
rs6658918	1.00[EUR][1000 genomes]
rs6659109	1.00[EUR][1000 genomes]
rs6674133	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6681611	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6687424	1.00[EUR][1000 genomes]
rs6691181	1.00[EUR][1000 genomes]
rs6702649	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73121865	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73123788	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73123791	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73124491	1.00[EUR][1000 genomes]
rs73124493	1.00[EUR][1000 genomes]
rs73125526	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73125529	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73125533	0.91[AFR][1000 genomes]
rs73125543	0.88[AFR][1000 genomes]
rs73126411	1.00[EUR][1000 genomes]
rs73128442	1.00[EUR][1000 genomes]
rs73133345	1.00[EUR][1000 genomes]
rs74146372	1.00[EUR][1000 genomes]
rs74146374	1.00[EUR][1000 genomes]
rs74146377	1.00[EUR][1000 genomes]
rs74146381	1.00[EUR][1000 genomes]
rs74146382	1.00[EUR][1000 genomes]
rs74146383	1.00[EUR][1000 genomes]
rs74146384	1.00[EUR][1000 genomes]
rs74146386	1.00[EUR][1000 genomes]
rs74146389	1.00[EUR][1000 genomes]
rs7512165	1.00[EUR][1000 genomes]
rs9661679	1.00[EUR][1000 genomes]
rs9661938	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	nsv8868	chr1:224383023-224752531	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv469889	chr1:224440354-224634374	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv482318	chr1:224440354-224634374	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224545200-224555200	Weak transcription	Spleen	Spleen
2	chr1:224545400-224559000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:224545600-224555200	Weak transcription	Lung	lung
4	chr1:224545600-224555200	Weak transcription	Ovary	ovary
5	chr1:224545800-224555000	Weak transcription	Brain Anterior Caudate	brain
6	chr1:224545800-224562800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:224545800-224605000	Weak transcription	Aorta	Aorta
8	chr1:224546000-224554600	Weak transcription	Liver	Liver
9	chr1:224546000-224555200	Weak transcription	Fetal Kidney	kidney
10	chr1:224546000-224556400	Weak transcription	Brain Angular Gyrus	brain
11	chr1:224546000-224563800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr1:224546000-224564400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:224546200-224554800	Weak transcription	Placenta	Placenta
14	chr1:224546200-224554800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:224546200-224555200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:224546200-224555200	Weak transcription	Brain Hippocampus Middle	brain
17	chr1:224546200-224555200	Weak transcription	Brain Substantia Nigra	brain
18	chr1:224546200-224555200	Weak transcription	Colonic Mucosa	Colon
19	chr1:224546200-224555200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr1:224546200-224555200	Weak transcription	Right Ventricle	heart
21	chr1:224546200-224555400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:224546400-224555200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:224546400-224555200	Weak transcription	Left Ventricle	heart
24	chr1:224546400-224555400	Weak transcription	Primary hematopoietic stem cells	blood
25	chr1:224546800-224554400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr1:224546800-224554800	Weak transcription	Hela-S3	cervix
27	chr1:224546800-224555200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr1:224546800-224558000	Weak transcription	NHLF	lung
29	chr1:224546800-224562200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr1:224547000-224554800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr1:224547000-224554800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:224547000-224555200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr1:224547000-224555200	Weak transcription	Brain Germinal Matrix	brain
34	chr1:224547000-224593200	Weak transcription	Stomach Mucosa	stomach
35	chr1:224547200-224555000	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr1:224547200-224555400	Weak transcription	Fetal Heart	heart
37	chr1:224547400-224554800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr1:224547400-224561800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr1:224547400-224618600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr1:224547600-224555200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr1:224547800-224555200	Weak transcription	Esophagus	oesophagus
42	chr1:224547800-224555200	Weak transcription	Gastric	stomach
43	chr1:224547800-224556400	Weak transcription	Right Atrium	heart
44	chr1:224547800-224562800	Weak transcription	Pancreas	Pancrea
45	chr1:224547800-224568600	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr1:224548000-224554800	Weak transcription	Fetal Brain Female	brain
47	chr1:224548000-224576000	Weak transcription	Fetal Brain Male	brain
48	chr1:224548600-224554400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr1:224548600-224554800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr1:224548800-224555000	Weak transcription	Stomach Smooth Muscle	stomach

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