Variant report

Variant	rs9516626
Chromosome Location	chr13:96586106-96586107
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:96586030..96588095-chr13:96594403..96597240,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1807900	0.84[EUR][1000 genomes]
rs1980942	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1996054	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2389531	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2774113	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3099360	0.85[ASN][1000 genomes]
rs34482628	0.82[EUR][1000 genomes]
rs472788	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs473930	0.89[EUR][1000 genomes]
rs4773930	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs493109	0.83[EUR][1000 genomes]
rs506474	0.87[EUR][1000 genomes]
rs517173	0.86[EUR][1000 genomes]
rs521235	0.90[EUR][1000 genomes]
rs529306	0.86[EUR][1000 genomes]
rs531090	0.87[EUR][1000 genomes]
rs532399	0.87[EUR][1000 genomes]
rs536606	0.87[EUR][1000 genomes]
rs539604	0.85[EUR][1000 genomes]
rs541811	0.89[EUR][1000 genomes]
rs544080	0.89[EUR][1000 genomes]
rs551457	0.89[EUR][1000 genomes]
rs552598	0.88[EUR][1000 genomes]
rs561996	0.87[EUR][1000 genomes]
rs566894	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs590758	0.90[EUR][1000 genomes]
rs592205	0.87[EUR][1000 genomes]
rs6492826	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7333045	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7992824	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs816139	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs816143	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9516629	0.82[EUR][1000 genomes]
rs9525081	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9525085	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9525086	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9525091	0.84[EUR][1000 genomes]
rs9525093	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9525098	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9561979	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9742440	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832691	chr13:96478098-96659823	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv900935	chr13:96497070-96631221	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1050430	chr13:96508530-97020734	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv541883	chr13:96508530-97020734	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1041165	chr13:96522021-96966520	Enhancers Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1051574	chr13:96550653-96779248	Strong transcription Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1040320	chr13:96573646-96790859	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9516626	DNAJC3	cis	Esophagus Muscularis	GTEx
rs9516626	UGCGL2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96495000-96590800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr13:96536200-96587200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr13:96543000-96586800	Weak transcription	Brain Hippocampus Middle	brain
4	chr13:96549400-96586400	Weak transcription	Hela-S3	cervix
5	chr13:96558400-96586600	Weak transcription	Right Ventricle	heart
6	chr13:96559600-96586400	Weak transcription	A549	lung
7	chr13:96559800-96588600	Weak transcription	Gastric	stomach
8	chr13:96566800-96587000	Weak transcription	Colon Smooth Muscle	Colon
9	chr13:96571000-96588600	Weak transcription	Psoas Muscle	Psoas
10	chr13:96577000-96623200	Weak transcription	NHLF	lung
11	chr13:96577200-96587600	Weak transcription	HepG2	liver
12	chr13:96577200-96598000	Weak transcription	HMEC	breast
13	chr13:96577800-96608800	Weak transcription	NHEK	skin
14	chr13:96579000-96587200	Weak transcription	NH-A	brain
15	chr13:96579000-96587600	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr13:96580800-96588600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr13:96581600-96586600	Weak transcription	Aorta	Aorta
18	chr13:96581600-96589000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr13:96581600-96589600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr13:96582000-96586400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr13:96582000-96587400	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr13:96582000-96587400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr13:96582200-96586400	Weak transcription	Liver	Liver
24	chr13:96582200-96587800	Weak transcription	Brain Angular Gyrus	brain
25	chr13:96582200-96588200	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr13:96582200-96588200	Weak transcription	Brain Substantia Nigra	brain
27	chr13:96582200-96588400	Weak transcription	Brain Anterior Caudate	brain
28	chr13:96582400-96586400	Weak transcription	Fetal Kidney	kidney
29	chr13:96582400-96586600	Weak transcription	Brain Germinal Matrix	brain
30	chr13:96582400-96586800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr13:96582400-96587800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr13:96582800-96586600	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr13:96583200-96586400	Weak transcription	Fetal Muscle Trunk	muscle
34	chr13:96583200-96586400	Weak transcription	HSMMtube	muscle
35	chr13:96583200-96586600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr13:96583200-96586600	Weak transcription	Osteobl	bone
37	chr13:96583200-96587200	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr13:96583200-96587800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr13:96583400-96586200	Weak transcription	HSMM	muscle
40	chr13:96583600-96586400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr13:96583600-96586400	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr13:96583600-96586600	Weak transcription	Adipose Nuclei	Adipose
43	chr13:96583600-96587000	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr13:96583600-96587600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr13:96583800-96586400	Weak transcription	Placenta	Placenta
46	chr13:96583800-96588600	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr13:96584000-96586600	Weak transcription	Ovary	ovary
48	chr13:96584000-96588200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr13:96584000-96599200	Weak transcription	Colonic Mucosa	Colon
50	chr13:96584200-96586200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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