Variant report

Variant	rs13039536
Chromosome Location	chr20:23612305-23612306
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:23332367..23335198-chr20:23611839..23614673,2	MCF-7	breast:
2	chr20:23610507..23612555-chr20:23613561..23616038,2	MCF-7	breast:
3	chr20:23610829..23612765-chr20:23625069..23626806,2	MCF-7	breast:
4	chr20:23593307..23595143-chr20:23609634..23612477,2	K562	blood:
5	chr20:23608610..23615599-chr20:23616056..23619619,19	MCF-7	breast:
6	chr20:23606151..23608595-chr20:23610355..23612719,2	K562	blood:
7	chr20:23603350..23604972-chr20:23610943..23612814,2	K562	blood:

Variant related genes	Relation type
ENSG00000269407	Chromatin interaction
ENSG00000101439	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs1010117	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1011226	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1064039	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1158167	0.86[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs12624424	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12625182	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12625716	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12710327	0.82[EUR][1000 genomes]
rs13037490	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs13038305	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13038337	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13038990	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13041070	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13043266	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13043610	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1555355	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17751897	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2016161	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2067488	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2208289	0.86[EUR][1000 genomes]
rs2254635	1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2405367	0.85[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2405392	0.86[CHB][hapmap];0.81[EUR][1000 genomes]
rs2405393	0.81[EUR][1000 genomes]
rs2424582	1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28703706	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3004139	0.86[EUR][1000 genomes]
rs3004145	0.86[EUR][1000 genomes]
rs3088162	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34374560	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34746357	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34792920	0.81[EUR][1000 genomes]
rs34897231	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34911568	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35488434	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35573837	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35610040	1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35782710	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35966482	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3761280	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3761281	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3787498	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3787499	1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3810575	0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs3827141	1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3827142	1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3827143	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4346460	0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs4815222	0.86[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs4815223	0.86[EUR][1000 genomes]
rs4815224	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5030707	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55897275	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56371840	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56388902	0.90[EUR][1000 genomes]
rs57549987	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59059917	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6036461	0.86[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs6036463	0.86[EUR][1000 genomes]
rs6036465	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6036469	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6036470	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6036471	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6036474	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6036476	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6036478	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6048920	0.86[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs6048922	0.86[EUR][1000 genomes]
rs6048923	0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs6048924	0.86[EUR][1000 genomes]
rs6048925	0.85[EUR][1000 genomes]
rs6048926	0.85[EUR][1000 genomes]
rs6048928	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs6048929	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6048930	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6048933	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6048936	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6048939	0.83[EUR][1000 genomes]
rs6048941	0.83[EUR][1000 genomes]
rs6048945	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6048946	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6048949	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6048950	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6048952	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6048956	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61035931	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6106685	0.85[EUR][1000 genomes]
rs6114201	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6114206	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6114208	1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6114209	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6515375	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67567111	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67997662	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71334202	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7265178	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7270413	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73318135	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs734801	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8114619	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8115417	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8115423	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8116859	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8121147	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8121283	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8121405	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs911119	1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491876	chr20:23436633-24031374	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13039536	CST3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23600600-23617000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr20:23602000-23616800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr20:23603800-23615400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr20:23604000-23612800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr20:23604000-23613000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr20:23604000-23613000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr20:23604000-23613400	Weak transcription	Brain Hippocampus Middle	brain
8	chr20:23604000-23614400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr20:23604000-23616600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr20:23604000-23616800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr20:23604200-23615000	Weak transcription	Brain Anterior Caudate	brain
12	chr20:23605000-23612800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr20:23606600-23615200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr20:23606600-23617000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr20:23606800-23616600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr20:23607000-23612600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr20:23607000-23615000	Weak transcription	Colon Smooth Muscle	Colon
18	chr20:23607200-23612800	Weak transcription	Gastric	stomach
19	chr20:23607400-23612600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr20:23607400-23612600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr20:23607600-23612600	Weak transcription	Pancreas	Pancrea
22	chr20:23607600-23615400	Weak transcription	Fetal Kidney	kidney
23	chr20:23608000-23612400	Weak transcription	Fetal Stomach	stomach
24	chr20:23608200-23614400	Weak transcription	Thymus	Thymus
25	chr20:23608800-23613400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr20:23609600-23612600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr20:23609600-23615000	Weak transcription	HSMMtube	muscle
28	chr20:23609800-23616800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr20:23610000-23613800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr20:23610200-23616800	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr20:23610200-23617000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr20:23610200-23617000	Weak transcription	K562	blood
33	chr20:23610400-23612400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr20:23610400-23612800	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr20:23610400-23612800	Weak transcription	NHEK	skin
36	chr20:23610400-23613400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr20:23610400-23613400	Weak transcription	Osteobl	bone
38	chr20:23610400-23613600	Weak transcription	HSMM	muscle
39	chr20:23610400-23613800	Weak transcription	Psoas Muscle	Psoas
40	chr20:23610400-23615400	Weak transcription	NHDF-Ad	bronchial
41	chr20:23610400-23616000	Weak transcription	Fetal Thymus	thymus
42	chr20:23610400-23616800	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr20:23610400-23616800	Weak transcription	NH-A	brain
44	chr20:23610400-23618200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr20:23610600-23612600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr20:23610600-23614400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr20:23610600-23616800	Weak transcription	Hela-S3	cervix
48	chr20:23610800-23612600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr20:23610800-23612600	Weak transcription	Placenta	Placenta
50	chr20:23610800-23615200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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