Variant report

Variant	rs62482404
Chromosome Location	chr7:102986977-102986978
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr7:102986885-102987128	A549	lung:	n/a	n/a
2	CEBPB	chr7:102986864-102987104	HepG2	liver:	n/a	n/a
3	STAT3	chr7:102986854-102987054	MCF10A-Er-Src	breast:	n/a	n/a
4	IRF1	chr7:102986962-102987258	K562	blood:	n/a	n/a
5	CEBPB	chr7:102986848-102987172	Hela-S3	cervix:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

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:

No data

Variant related genes	Relation type
DNAJC2	TF binding region
PSMC2	TF binding region
ENSG00000235354	TF binding region
ENSG00000161057	Chromatin interaction
ENSG00000105819	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	0.96[ASN][1000 genomes]
rs11978339	1.00[ASN][1000 genomes]
rs17136728	1.00[ASN][1000 genomes]
rs17680523	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3087615	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35399723	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4729911	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62482370	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62482394	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62482397	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62482398	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62482399	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62482403	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62482405	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62482406	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6972190	0.85[ASN][1000 genomes]
rs73175837	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73175852	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[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
rs62482404	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	chr7:102985200-102987200	Weak transcription	Fetal Heart	heart
2	chr7:102985200-102987200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr7:102985200-102987200	Weak transcription	Small Intestine	intestine
4	chr7:102985200-102988000	Weak transcription	Gastric	stomach
5	chr7:102985400-102987600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr7:102985400-102987600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr7:102985400-102987600	Weak transcription	Fetal Muscle Trunk	muscle
8	chr7:102985400-102987600	Weak transcription	Pancreas	Pancrea
9	chr7:102985400-102987800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr7:102985400-102987800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr7:102985400-102987800	Weak transcription	Esophagus	oesophagus
12	chr7:102985400-102987800	Weak transcription	Left Ventricle	heart
13	chr7:102985400-102988000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr7:102985400-102988000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr7:102985400-102988000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr7:102985400-102988000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr7:102985400-102988000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr7:102985400-102988000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr7:102985400-102988000	Weak transcription	Lung	lung
20	chr7:102985400-102988000	Weak transcription	Spleen	Spleen
21	chr7:102985600-102987200	Weak transcription	Primary B cells from peripheral blood	blood
22	chr7:102985600-102987200	Weak transcription	Fetal Brain Male	brain
23	chr7:102985600-102987400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr7:102985600-102987400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr7:102985600-102987400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr7:102985600-102987400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr7:102985600-102987400	Weak transcription	Fetal Muscle Leg	muscle
28	chr7:102985600-102987400	Weak transcription	Fetal Stomach	stomach
29	chr7:102985600-102987400	Weak transcription	Fetal Thymus	thymus
30	chr7:102985600-102987400	Weak transcription	Right Ventricle	heart
31	chr7:102985600-102987400	Weak transcription	HSMM	muscle
32	chr7:102985600-102987400	Weak transcription	HSMMtube	muscle
33	chr7:102985600-102987600	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr7:102985600-102987600	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr7:102985600-102987600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr7:102985600-102987600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr7:102985600-102987600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr7:102985600-102987600	Weak transcription	Brain Germinal Matrix	brain
39	chr7:102985600-102987600	Weak transcription	Colonic Mucosa	Colon
40	chr7:102985600-102987600	Weak transcription	Placenta	Placenta
41	chr7:102985600-102987600	Weak transcription	Psoas Muscle	Psoas
42	chr7:102985600-102987600	Weak transcription	Right Atrium	heart
43	chr7:102985600-102987600	Weak transcription	Stomach Mucosa	stomach
44	chr7:102985600-102987800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr7:102985600-102987800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr7:102985600-102987800	Weak transcription	Aorta	Aorta
47	chr7:102985600-102987800	Weak transcription	Ovary	ovary
48	chr7:102985800-102987000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr7:102985800-102987000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr7:102985800-102987000	Weak transcription	Colon Smooth Muscle	Colon

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