Variant report

Variant	rs72698960
Chromosome Location	chr1:152413579-152413580
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:152160983..152163280-chr1:152412961..152414390,15	MCF-7	breast:
2	chr1:152160785..152161519-chr1:152413069..152413968,2	K562	blood:
3	chr1:152024764..152025483-chr1:152413415..152413970,2	K562	blood:
4	chr1:152370937..152372499-chr1:152412540..152414323,43	MCF-7	breast:
5	chr1:152161080..152162827-chr1:152413067..152413987,7	MCF-7	breast:
6	chr1:152369672..152370659-chr1:152413047..152413901,4	MCF-7	breast:
7	chr1:152412473..152414075-chr1:152416605..152419173,2	K562	blood:
8	chr1:152370764..152372337-chr1:152412999..152414162,14	MCF-7	breast:
9	chr1:152319630..152320287-chr1:152413308..152413947,2	MCF-7	breast:
10	chr1:152379306..152381264-chr1:152411990..152414045,3	MCF-7	breast:
11	chr1:152370558..152373181-chr1:152412666..152414314,2	MCF-7	breast:
12	chr1:152162395..152164443-chr1:152410728..152413718,2	MCF-7	breast:
13	chr1:152368385..152370359-chr1:152413395..152416053,2	MCF-7	breast:
14	chr1:152413209..152414030-chr1:152423642..152424387,3	MCF-7	breast:
15	chr1:152160487..152160988-chr1:152413455..152414286,2	MCF-7	breast:
16	chr1:152369903..152370605-chr1:152413321..152413987,3	MCF-7	breast:
17	chr1:152413332..152413978-chr1:152430103..152431369,3	MCF-7	breast:
18	chr1:152413327..152415883-chr1:152427595..152432391,4	MCF-7	breast:
19	chr1:152162203..152163021-chr1:152413054..152413609,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000183586	Chromatin interaction
ENSG00000237975	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11577946	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11579266	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12067942	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1923501	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2146117	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36061814	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs499997	0.80[AFR][1000 genomes]
rs556124	0.80[AFR][1000 genomes]
rs56325026	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6696556	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72698953	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72698963	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72698964	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72698999	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014095	chr1:152104486-152454591	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1005472	chr1:152247763-152443448	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv535161	chr1:152247763-152443448	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv916016	chr1:152337775-152590520	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv872443	chr1:152400055-152459747	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv872444	chr1:152400361-152440753	ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv824664	chr1:152409024-152434443	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv463850	chr1:152411090-152434009	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv547858	chr1:152411090-152434009	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv872445	chr1:152411813-152440753	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs72698960	CRNN	cis	Esophagus Mucosa	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152409400-152414800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr1:152409600-152414600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:152409800-152416600	Weak transcription	HSMM	muscle
4	chr1:152410200-152415400	Weak transcription	HSMMtube	muscle
5	chr1:152410600-152413600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:152413000-152413800	Enhancers	HMEC	breast
7	chr1:152413000-152416400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:152413200-152413600	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr1:152413200-152413600	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr1:152413200-152413600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
11	chr1:152413200-152413600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr1:152413200-152413600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr1:152413200-152413600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:152413200-152413600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr1:152413200-152413600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:152413200-152413600	Enhancers	Duodenum Mucosa	Duodenum
17	chr1:152413200-152413600	Enhancers	Lung	lung
18	chr1:152413200-152413600	Enhancers	Ovary	ovary
19	chr1:152413200-152413600	Enhancers	Pancreas	Pancrea
20	chr1:152413200-152413600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
21	chr1:152413200-152413800	Enhancers	Primary B cells from peripheral blood	blood
22	chr1:152413200-152413800	Enhancers	Brain Angular Gyrus	brain
23	chr1:152413200-152413800	Enhancers	Brain Cingulate Gyrus	brain
24	chr1:152413200-152413800	Enhancers	Rectal Smooth Muscle	rectum
25	chr1:152413200-152414400	Enhancers	Fetal Stomach	stomach
26	chr1:152413200-152415200	Enhancers	NHEK	skin
27	chr1:152413400-152413600	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr1:152413400-152413600	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr1:152413400-152413800	Weak transcription	Esophagus	oesophagus
30	chr1:152413400-152413800	Enhancers	A549	lung
31	chr1:152413400-152414000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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