Variant report

Variant	rs62482405
Chromosome Location	chr7:102987583-102987584
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	MAX	chr7:102987442-102987630	K562	blood:	n/a	n/a
2	CCNT2	chr7:102987416-102987584	K562	blood:	n/a	n/a
3	MYC	chr7:102987481-102988690	K562	blood:	n/a	chr7:102988233-102988242
4	HCFC1	chr7:102987446-102988837	Hela-S3	cervix:	n/a	n/a
5	GABPA	chr7:102987562-102988785	SK-N-SH	brain:	n/a	n/a
6	GABPA	chr7:102987383-102988703	A549	lung:	n/a	n/a
7	POLR2A	chr7:102987456-102988674	GM12891	blood:	n/a	n/a
8	MYC	chr7:102987566-102988603	K562	blood:	n/a	chr7:102988233-102988242
9	BRCA1	chr7:102987576-102988290	Hela-S3	cervix:	n/a	n/a
10	MXI1	chr7:102987272-102989184	SK-N-SH	brain:	n/a	n/a
11	MYC	chr7:102987567-102988574	K562	blood:	n/a	chr7:102988233-102988242
12	POLR2A	chr7:102987555-102988560	Raji	blood:	n/a	n/a
13	GABPA	chr7:102987559-102988669	HL-60	blood:	n/a	n/a
14	MAX	chr7:102987551-102988677	Hela-S3	cervix:	n/a	chr7:102988233-102988242
15	MAX	chr7:102987400-102987773	K562	blood:	n/a	n/a
16	REST	chr7:102987558-102988844	H1-neurons	neurons:	n/a	chr7:102988111-102988119 chr7:102988012-102988021 chr7:102988574-102988584
17	POLR2A	chr7:102987542-102988607	K562	blood:	n/a	n/a
18	MYC	chr7:102987500-102988347	MCF10A-Er-Src	breast:	n/a	chr7:102988233-102988242
19	TRIM28	chr7:102987484-102988673	K562	blood:	n/a	n/a
20	POLR2A	chr7:102987583-102987614	HepG2	liver:	n/a	n/a
21	POLR2A	chr7:102987517-102988566	GM12878	blood:	n/a	n/a
22	MAX	chr7:102987579-102988802	NB4	blood:	n/a	chr7:102988233-102988242
23	MXI1	chr7:102987474-102988677	GM12878	blood:	n/a	n/a
24	POLR2A	chr7:102987458-102988556	PBDE	blood:	n/a	n/a
25	POLR2A	chr7:102987469-102987606	GM12878	blood:	n/a	n/a
26	POLR2A	chr7:102987395-102988622	SK-N-MC	brain:	n/a	n/a
27	POLR2A	chr7:102987562-102988602	K562	blood:	n/a	n/a
28	TBP	chr7:102987441-102988400	Hela-S3	cervix:	n/a	n/a
29	YY1	chr7:102987486-102987685	K562	blood:	n/a	n/a
30	POLR2A	chr7:102987546-102988626	PFSK-1	brain:	n/a	n/a
31	GABPA	chr7:102987364-102989043	MCF-7	breast:	n/a	n/a
32	SIN3AK20	chr7:102987250-102988940	MCF-7	breast:	n/a	n/a
33	POLR2A	chr7:102987435-102988594	K562	blood:	n/a	n/a
34	NR2F2	chr7:102987083-102988712	K562	blood:	n/a	n/a
35	GABPA	chr7:102987390-102988723	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:102986418..102988038-chr7:103002677..103005310,2	MCF-7	breast:
2	chr7:102985801..102988049-chr7:103030466..103032133,2	K562	blood:
3	chr7:102967942..102969803-chr7:102985460..102987931,2	MCF-7	breast:
4	chr7:102937260..102939405-chr7:102983367..102989226,6	MCF-7	breast:
5	chr7:102983625..102990524-chr7:102994295..102998538,7	MCF-7	breast:
6	chr7:102937219..102940435-chr7:102985734..102988691,4	MCF-7	breast:
7	chr7:102936427..102940589-chr7:102983649..102988902,7	K562	blood:

Variant related genes	Relation type
PSMC2	TF binding region
ENSG00000235354	TF binding region
DNAJC2	TF binding region
ENSG00000105819	Chromatin interaction
ENSG00000161057	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10271758	0.91[ASN][1000 genomes]
rs11978339	0.96[ASN][1000 genomes]
rs17136728	0.96[ASN][1000 genomes]
rs17680523	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3087615	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35399723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4729911	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62482370	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62482394	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62482397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62482398	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62482399	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62482403	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62482404	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62482406	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6972190	0.81[ASN][1000 genomes]
rs73175837	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73175852	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868996	chr7:102332827-102991361	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1030446	chr7:102932689-103221638	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv491911	chr7:102967150-103403622	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62482405	RP11-401L13.5	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102985200-102988000	Weak transcription	Gastric	stomach
2	chr7:102985400-102987600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr7:102985400-102987600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr7:102985400-102987600	Weak transcription	Fetal Muscle Trunk	muscle
5	chr7:102985400-102987600	Weak transcription	Pancreas	Pancrea
6	chr7:102985400-102987800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr7:102985400-102987800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr7:102985400-102987800	Weak transcription	Esophagus	oesophagus
9	chr7:102985400-102987800	Weak transcription	Left Ventricle	heart
10	chr7:102985400-102988000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr7:102985400-102988000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr7:102985400-102988000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr7:102985400-102988000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr7:102985400-102988000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr7:102985400-102988000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr7:102985400-102988000	Weak transcription	Lung	lung
17	chr7:102985400-102988000	Weak transcription	Spleen	Spleen
18	chr7:102985600-102987600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr7:102985600-102987600	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr7:102985600-102987600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr7:102985600-102987600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr7:102985600-102987600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr7:102985600-102987600	Weak transcription	Brain Germinal Matrix	brain
24	chr7:102985600-102987600	Weak transcription	Colonic Mucosa	Colon
25	chr7:102985600-102987600	Weak transcription	Placenta	Placenta
26	chr7:102985600-102987600	Weak transcription	Psoas Muscle	Psoas
27	chr7:102985600-102987600	Weak transcription	Right Atrium	heart
28	chr7:102985600-102987600	Weak transcription	Stomach Mucosa	stomach
29	chr7:102985600-102987800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr7:102985600-102987800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr7:102985600-102987800	Weak transcription	Aorta	Aorta
32	chr7:102985600-102987800	Weak transcription	Ovary	ovary
33	chr7:102985800-102987600	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr7:102985800-102987600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr7:102985800-102987600	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr7:102985800-102987600	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr7:102985800-102987600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr7:102985800-102987600	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr7:102985800-102987600	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr7:102985800-102987600	Weak transcription	Fetal Intestine Large	intestine
41	chr7:102985800-102987600	Weak transcription	Fetal Kidney	kidney
42	chr7:102985800-102987600	Weak transcription	Thymus	Thymus
43	chr7:102985800-102987800	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr7:102986000-102987600	Weak transcription	Fetal Intestine Small	intestine
45	chr7:102986800-102987600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr7:102986800-102987800	Flanking Active TSS	Hela-S3	cervix
47	chr7:102987000-102987600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr7:102987000-102987600	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr7:102987000-102987600	Enhancers	Colon Smooth Muscle	Colon
50	chr7:102987000-102987800	Flanking Active TSS	GM12878-XiMat	blood

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