Variant report

Variant	rs4597197
Chromosome Location	chr13:76017101-76017102
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:76016614..76019558-chr13:76031564..76033175,2	MCF-7	breast:
2	chr13:76010975..76013895-chr13:76015597..76017378,2	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs4331237	0.87[ASN][1000 genomes]
rs4331238	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4369537	0.88[ASN][1000 genomes]
rs4530003	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs718147	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7334537	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7983963	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7985929	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7995759	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9318345	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9530437	0.87[ASN][1000 genomes]
rs9530438	0.94[ASN][1000 genomes]
rs9543927	0.87[ASN][1000 genomes]
rs9543928	0.93[ASN][1000 genomes]
rs9543929	0.92[ASN][1000 genomes]
rs9573541	0.88[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	esv2761803	chr13:75943309-76161774	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv455987	chr13:75972846-76090084	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv562346	chr13:75972846-76090084	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4597197	JARID2	trans	lymphoblastoid	seeQTL
rs4597197	UCHL3	cis	parietal	SCAN
rs4597197	RECQL4	trans	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76005200-76017200	Weak transcription	Pancreas	Pancrea
2	chr13:76005200-76017600	Weak transcription	Right Atrium	heart
3	chr13:76007400-76017600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr13:76007400-76018600	Weak transcription	Esophagus	oesophagus
5	chr13:76007400-76032000	Weak transcription	Gastric	stomach
6	chr13:76012000-76019800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr13:76012000-76033000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr13:76012400-76017600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr13:76012600-76019000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr13:76012800-76017200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr13:76012800-76017400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr13:76012800-76036000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr13:76014000-76017400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr13:76014000-76019400	Weak transcription	NHEK	skin
15	chr13:76014200-76017200	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr13:76014600-76019400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr13:76014600-76020000	Weak transcription	A549	lung
18	chr13:76014800-76017200	Weak transcription	Fetal Kidney	kidney
19	chr13:76014800-76021800	Enhancers	HepG2	liver
20	chr13:76015000-76017200	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr13:76015400-76017600	Weak transcription	Left Ventricle	heart
22	chr13:76016000-76017200	Weak transcription	Psoas Muscle	Psoas
23	chr13:76016200-76017200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr13:76016800-76017200	Active TSS	Ovary	ovary
25	chr13:76016800-76017400	Enhancers	Fetal Muscle Trunk	muscle
26	chr13:76016800-76018000	Enhancers	Fetal Lung	lung
27	chr13:76016800-76018200	Enhancers	Colon Smooth Muscle	Colon
28	chr13:76016800-76019200	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr13:76017000-76017200	Enhancers	NHLF	lung
30	chr13:76017000-76017600	Enhancers	Liver	Liver
31	chr13:76017000-76017800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr13:76017000-76017800	Enhancers	Fetal Stomach	stomach
33	chr13:76017000-76017800	Enhancers	K562	blood
34	chr13:76017000-76018000	Enhancers	Adipose Nuclei	Adipose
35	chr13:76017000-76018000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr13:76017000-76018000	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr13:76017000-76018000	Enhancers	Fetal Muscle Leg	muscle
38	chr13:76017000-76018800	Enhancers	Fetal Heart	heart

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