Variant report

Variant	rs60965269
Chromosome Location	chr10:51829520-51829521
allele	C/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	POLR2A	chr10:51829513-51829525	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000235618	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1072794	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10762973	0.87[EUR][1000 genomes]
rs10762975	0.87[EUR][1000 genomes]
rs12571765	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2009551	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2338056	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2338059	0.91[EUR][1000 genomes]
rs2805111	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs3886108	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3964873	0.92[EUR][1000 genomes]
rs3964886	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4301736	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56106241	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs57052909	0.90[AMR][1000 genomes]
rs58186870	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs60293935	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60539478	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61418463	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6481013	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7069872	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7074294	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7088088	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7097164	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71508040	0.85[AMR][1000 genomes]
rs73315603	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs74131213	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs74131214	0.85[AMR][1000 genomes]
rs7894916	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7902594	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7905304	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7905974	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7906068	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7915651	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758219	chr10:50971974-51925166	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	esv2759749	chr10:50971974-51925166	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv428232	chr10:50971974-51925166	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	esv1830900	chr10:51187411-51903662	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv518071	chr10:51595893-52157935	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	esv3521278	chr10:51635096-52001994	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	esv3521279	chr10:51635096-52001994	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs60965269	FAM21A	cis	Muscle Skeletal	GTEx
rs60965269	FAM21A	cis	Esophagus Mucosa	GTEx

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:51828000-51837200	Weak transcription	Spleen	Spleen
2	chr10:51828200-51837400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr10:51828400-51830000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr10:51828400-51830600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr10:51828400-51834600	Weak transcription	Gastric	stomach
6	chr10:51828400-51836000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr10:51828400-51837200	Weak transcription	Lung	lung
8	chr10:51828400-51837200	Weak transcription	HSMMtube	muscle
9	chr10:51828400-51837400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr10:51828400-51837600	Weak transcription	Brain Substantia Nigra	brain
11	chr10:51828400-51837800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr10:51828400-51853800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr10:51828600-51829600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr10:51828600-51829600	Weak transcription	HUVEC	blood vessel
15	chr10:51828600-51829800	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr10:51828600-51829800	Weak transcription	NH-A	brain
17	chr10:51828600-51829800	Weak transcription	NHDF-Ad	bronchial
18	chr10:51828600-51829800	Weak transcription	NHEK	skin
19	chr10:51828600-51830400	Weak transcription	Brain Angular Gyrus	brain
20	chr10:51828600-51830400	Weak transcription	Fetal Brain Female	brain
21	chr10:51828600-51830600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr10:51828600-51831200	Weak transcription	Brain Hippocampus Middle	brain
23	chr10:51828600-51834000	Weak transcription	Liver	Liver
24	chr10:51828600-51835000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr10:51828600-51835800	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr10:51828600-51835800	Weak transcription	Brain Anterior Caudate	brain
27	chr10:51828600-51835800	Weak transcription	Fetal Intestine Large	intestine
28	chr10:51828600-51836800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr10:51828600-51837200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr10:51828600-51837400	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr10:51828600-51837400	Weak transcription	Fetal Muscle Trunk	muscle
32	chr10:51828600-51837400	Weak transcription	Placenta	Placenta
33	chr10:51828600-51837600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr10:51828600-51837600	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr10:51828600-51837600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr10:51828600-51837600	Weak transcription	Primary B cells from peripheral blood	blood
37	chr10:51828600-51837600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr10:51828600-51837600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr10:51828600-51837600	Weak transcription	Fetal Thymus	thymus
40	chr10:51828600-51837600	Weak transcription	Thymus	Thymus
41	chr10:51828600-51837800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr10:51828600-51837800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr10:51828600-51838000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr10:51828600-51838000	Weak transcription	Fetal Stomach	stomach
45	chr10:51828600-51891800	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr10:51828600-51893400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr10:51828800-51829600	Enhancers	Primary T helper cells fromperipheralblood	blood
48	chr10:51828800-51830600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr10:51828800-51830800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr10:51828800-51832600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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