Variant report

Variant	rs60627429
Chromosome Location	chr1:224568762-224568763
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:224544249..224546691-chr1:224567251..224568815,2	K562	blood:
2	chr1:224568653..224571407-chr1:224574345..224577336,2	MCF-7	breast:
3	chr1:224550099..224552705-chr1:224565403..224568845,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143771	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10495218	0.90[AFR][1000 genomes]
rs10495221	0.92[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	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11809688	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11809710	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11810160	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11811935	1.00[EUR][1000 genomes]
rs11812007	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12239466	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	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16847784	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16847858	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16847870	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16847871	0.93[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	0.84[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	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57469223	1.00[EUR][1000 genomes]
rs57719044	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57967341	1.00[EUR][1000 genomes]
rs58304668	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58649883	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58788859	1.00[EUR][1000 genomes]
rs58814229	1.00[EUR][1000 genomes]
rs59034185	1.00[EUR][1000 genomes]
rs59561838	1.00[EUR][1000 genomes]
rs59577766	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59710928	1.00[EUR][1000 genomes]
rs59734390	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs60063902	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs60349703	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60715845	1.00[EUR][1000 genomes]
rs60831135	1.00[EUR][1000 genomes]
rs61000820	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61155217	1.00[EUR][1000 genomes]
rs61278437	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61590597	0.82[AFR][1000 genomes]
rs6426167	1.00[EUR][1000 genomes]
rs6658918	1.00[EUR][1000 genomes]
rs6659109	1.00[EUR][1000 genomes]
rs6674133	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6681611	0.82[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	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73121865	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73123788	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73123791	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73125526	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73125529	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73125533	0.87[AFR][1000 genomes]
rs73125540	0.80[AFR][1000 genomes]
rs73125543	0.83[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:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224545800-224605000	Weak transcription	Aorta	Aorta
2	chr1:224547000-224593200	Weak transcription	Stomach Mucosa	stomach
3	chr1:224547400-224618600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:224548000-224576000	Weak transcription	Fetal Brain Male	brain
5	chr1:224553800-224568800	Strong transcription	Fetal Stomach	stomach
6	chr1:224555800-224581400	Weak transcription	Fetal Heart	heart
7	chr1:224556000-224591000	Weak transcription	Small Intestine	intestine
8	chr1:224562800-224569600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:224563000-224577200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:224563000-224593400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:224563600-224571200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:224564600-224576600	Weak transcription	Ovary	ovary
13	chr1:224565000-224575000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr1:224565000-224575800	Weak transcription	Brain Angular Gyrus	brain
15	chr1:224565000-224576800	Weak transcription	NHEK	skin
16	chr1:224565000-224577200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:224565000-224577200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr1:224565000-224577200	Weak transcription	Colonic Mucosa	Colon
19	chr1:224565000-224577200	Weak transcription	Pancreas	Pancrea
20	chr1:224565000-224577200	Weak transcription	Spleen	Spleen
21	chr1:224565000-224581200	Weak transcription	Right Ventricle	heart
22	chr1:224565000-224582600	Weak transcription	Esophagus	oesophagus
23	chr1:224565000-224586200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr1:224565200-224572000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:224565200-224572400	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr1:224565200-224574600	Weak transcription	Colon Smooth Muscle	Colon
27	chr1:224565200-224576000	Weak transcription	Hela-S3	cervix
28	chr1:224565400-224577000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr1:224565600-224569000	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr1:224565600-224575000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr1:224565800-224569800	Weak transcription	NH-A	brain
32	chr1:224565800-224576600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr1:224566000-224568800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr1:224566000-224574600	Weak transcription	NHLF	lung
35	chr1:224566000-224576000	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr1:224566000-224576800	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr1:224566200-224573200	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr1:224566200-224575000	Weak transcription	Left Ventricle	heart
39	chr1:224566200-224576400	Weak transcription	HepG2	liver
40	chr1:224566200-224577000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr1:224566200-224577200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr1:224566400-224577800	Weak transcription	Fetal Intestine Small	intestine
43	chr1:224566800-224568800	Genic enhancers	Duodenum Mucosa	Duodenum
44	chr1:224567000-224577400	Weak transcription	Lung	lung
45	chr1:224567000-224577600	Weak transcription	Gastric	stomach
46	chr1:224567000-224579600	Weak transcription	Psoas Muscle	Psoas
47	chr1:224567200-224573800	Weak transcription	Liver	Liver
48	chr1:224567200-224574000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr1:224567200-224574000	Weak transcription	Adipose Nuclei	Adipose
50	chr1:224567200-224574800	Weak transcription	A549	lung

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