Variant report

Variant	rs36123979
Chromosome Location	chr3:23313730-23313731
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:23313519-23313884	MCF-7	breast:	n/a	n/a
2	MYC	chr3:23313705-23313733	MCF-7	breast:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:23313729-23313779	HRPEpiC	eye:	n/a
2	chr3:23313729-23313779	PFSK-1	brain:	n/a
3	chr3:23313729-23313779	NT2-D1	testis:	n/a
4	chr3:23313729-23313779	GM12891	blood:	n/a
5	chr3:23313729-23313779	Jurkat	blood:	n/a
6	chr3:23313729-23313779	HIPEpiC	eye:	n/a
7	chr3:23313729-23313779	HCF	heart:	n/a
8	chr3:23313729-23313779	GM12892	blood:	n/a
9	chr3:23313729-23313779	SK-N-MC	brain:	n/a
10	chr3:23313729-23313779	PANC-1	pancreas:	n/a
11	chr3:23313729-23313779	T-47D	breast:	n/a
12	chr3:23313729-23313779	RPTEC	kidney:	n/a
13	chr3:23313729-23313779	PrEC	prostate:	n/a
14	chr3:23313729-23313779	H1-hESC	embryonic stem cell:	embryo
15	chr3:23313729-23313779	HNPCEpiC	eye:	n/a
16	chr3:23313729-23313779	AG10803	skin:	n/a
17	chr3:23313729-23313779	HCM	heart:	n/a
18	chr3:23313729-23313779	ovcar-3	ovarian:	n/a
19	chr3:23313729-23313779	LNCaP	prostate:	n/a
20	chr3:23313729-23313779	SK-N-SH	brain:	n/a
21	chr3:23313729-23313779	BE2_C	brain:	n/a
22	chr3:23313729-23313779	HRE	kidney:	n/a
23	chr3:23313729-23313779	GM06990	blood:	n/a
24	chr3:23313729-23313779	BJ	skin:	n/a
25	chr3:23313729-23313779	Caco-2	colon:	n/a
26	chr3:23313729-23313779	NHBE	bronchial:	n/a
27	chr3:23313729-23313779	HPAEpiC	pulmonary alveolar:	n/a
28	chr3:23313729-23313779	SKMC	muscle:	n/a
29	chr3:23313729-23313779	HEK293	kidney:	embryo
30	chr3:23313729-23313779	NH-A	brain:	n/a
31	chr3:23313729-23313779	SK-N-SH_RA	brain:	n/a
32	chr3:23313729-23313779	A549	lung:	n/a
33	chr3:23313729-23313779	CMK	blood:	n/a
34	chr3:23313729-23313779	IMR90	lung:	fetal
35	chr3:23313729-23313779	Hela-S3	cervix:	n/a
36	chr3:23313729-23313779	AG04449	skin:	fetal
37	chr3:23313729-23313779	HMEC	breast:	n/a
38	chr3:23313729-23313779	AG09319	gingival:	n/a
39	chr3:23313729-23313779	K562	blood:	n/a
40	chr3:23313729-23313779	HL-60	blood:	n/a
41	chr3:23313729-23313779	HCT-116	colon:	n/a
42	chr3:23313729-23313779	MCF10A-Er-Src	breast:	n/a
43	chr3:23313729-23313779	AoSMC	blood vessel:	n/a
44	chr3:23313729-23313779	GM12878	blood:	n/a
45	chr3:23313729-23313779	ProgFib	skin:	n/a
46	chr3:23313729-23313779	HEEpiC	esophagus:	n/a
47	chr3:23313729-23313779	AG09309	skin:	n/a
48	chr3:23313729-23313779	Hepatocyte	liver:	n/a
49	chr3:23313729-23313779	NHDF-neo	bronchial:	n/a
50	chr3:23313729-23313779	GM19239	blood:	n/a

No data

Variant related genes	Relation type
ENSG00000206728	TF binding region
ENSG00000206728	CpG island

Extended variants
information (count: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs12106681	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13059155	0.88[EUR][1000 genomes]
rs13060112	0.85[EUR][1000 genomes]
rs13060251	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13063185	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13063451	0.86[EUR][1000 genomes]
rs13066741	0.88[EUR][1000 genomes]
rs13067514	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13073761	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13076527	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13078970	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13084250	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13085266	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13087238	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13087563	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13090335	0.88[EUR][1000 genomes]
rs13090633	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13092830	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13096187	0.88[EUR][1000 genomes]
rs13099586	0.81[EUR][1000 genomes]
rs13100499	0.86[EUR][1000 genomes]
rs13100605	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34134134	0.88[EUR][1000 genomes]
rs34322396	0.86[EUR][1000 genomes]
rs34443476	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34474308	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34504120	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34513914	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34584255	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34619482	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34732257	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34743949	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34758087	0.88[EUR][1000 genomes]
rs34804976	0.86[EUR][1000 genomes]
rs34827773	0.85[EUR][1000 genomes]
rs34894979	0.86[EUR][1000 genomes]
rs34916096	0.88[EUR][1000 genomes]
rs34928966	0.88[EUR][1000 genomes]
rs35021696	0.86[EUR][1000 genomes]
rs35024744	0.81[EUR][1000 genomes]
rs35028631	0.88[EUR][1000 genomes]
rs35055753	0.88[EUR][1000 genomes]
rs35096750	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35156003	0.88[EUR][1000 genomes]
rs35177750	0.86[EUR][1000 genomes]
rs35179250	0.88[EUR][1000 genomes]
rs35190363	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35218978	0.88[EUR][1000 genomes]
rs35230557	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35240920	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35245309	0.88[EUR][1000 genomes]
rs35266274	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35273607	0.88[EUR][1000 genomes]
rs35314441	0.88[EUR][1000 genomes]
rs35346188	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35347265	0.88[EUR][1000 genomes]
rs35383024	0.86[EUR][1000 genomes]
rs35402533	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35408638	0.88[EUR][1000 genomes]
rs35497505	0.88[EUR][1000 genomes]
rs35587590	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35649850	0.85[EUR][1000 genomes]
rs35657558	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35776486	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35778452	0.86[EUR][1000 genomes]
rs35869522	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35892300	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35902312	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35907941	0.85[EUR][1000 genomes]
rs35928592	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35975795	0.88[EUR][1000 genomes]
rs36060079	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs36124326	0.88[EUR][1000 genomes]
rs58522464	0.86[EUR][1000 genomes]
rs60074421	0.86[EUR][1000 genomes]
rs71317817	0.89[AMR][1000 genomes]
rs71317819	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71317820	0.85[EUR][1000 genomes]
rs71317821	0.85[EUR][1000 genomes]
rs71317822	0.85[EUR][1000 genomes]
rs71317823	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71317824	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71317827	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71317829	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71317834	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs71322171	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71322172	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71322173	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71322174	0.88[EUR][1000 genomes]
rs71322183	0.88[EUR][1000 genomes]
rs71322184	0.88[EUR][1000 genomes]
rs71322185	0.86[EUR][1000 genomes]
rs71322187	0.86[EUR][1000 genomes]
rs71322189	0.86[EUR][1000 genomes]
rs71322190	0.84[EUR][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	nsv1014701	chr3:23257658-23416094	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv589947	chr3:23277838-23403943	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1002823	chr3:23277838-23623083	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv589948	chr3:23287141-23390221	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23295200-23321800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr3:23298800-23336600	Weak transcription	Thymus	Thymus
3	chr3:23299000-23314200	Weak transcription	Primary T cells from cord blood	blood
4	chr3:23302400-23321000	Weak transcription	Pancreas	Pancrea
5	chr3:23305600-23318400	Weak transcription	Brain Substantia Nigra	brain
6	chr3:23306800-23314200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:23307200-23314400	Weak transcription	HSMMtube	muscle
8	chr3:23307200-23316000	Weak transcription	Primary B cells from cord blood	blood
9	chr3:23312000-23316800	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:23312400-23314800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:23312600-23314000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr3:23312800-23313800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:23312800-23314000	ZNF genes & repeats	Lung	lung
14	chr3:23312800-23314200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:23312800-23314200	ZNF genes & repeats	Fetal Stomach	stomach
16	chr3:23312800-23314400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:23313200-23314000	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:23313200-23314000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:23313200-23314400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:23313400-23313800	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:23313400-23314000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:23313400-23314000	ZNF genes & repeats	Spleen	Spleen
23	chr3:23313400-23314200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
24	chr3:23313400-23314400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:23313400-23314600	ZNF genes & repeats	GM12878-XiMat	blood
26	chr3:23313600-23314000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr3:23313600-23314400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr3:23313600-23314400	Weak transcription	Primary B cells from peripheral blood	blood

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