Variant report

Variant	rs6036474
Chromosome Location	chr20:23604414-23604415
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	chr20:23603693..23605548-chr20:23605615..23607306,2	MCF-7	breast:
2	chr20:23603350..23604972-chr20:23610943..23612814,2	K562	blood:

Extended variants
information (count: 110 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs1010117	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1011226	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1064039	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1158167	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes]
rs12624424	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12625182	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12625716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12710327	0.85[EUR][1000 genomes]
rs13037490	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13038305	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13038337	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13038990	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13039536	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13040663	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13041070	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13043266	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13043610	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1555355	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17751897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2016161	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2067488	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2208289	0.89[EUR][1000 genomes]
rs2254635	0.84[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2405367	0.85[CEU][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2405392	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs2405393	0.85[EUR][1000 genomes]
rs2424582	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28703706	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3004139	0.89[EUR][1000 genomes]
rs3004145	0.89[EUR][1000 genomes]
rs3088162	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34374560	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34746357	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34792920	0.84[EUR][1000 genomes]
rs34897231	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34911568	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35488434	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35573837	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35610040	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35782710	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35966482	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3761280	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3761281	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3787498	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3787499	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3810575	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3827141	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3827142	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3827143	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4346460	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[EUR][1000 genomes]
rs4815222	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes]
rs4815223	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs4815224	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5030707	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55897275	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56077567	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56371840	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56388902	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57549987	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59059917	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6036461	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes]
rs6036463	0.89[EUR][1000 genomes]
rs6036465	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6036469	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6036470	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6036471	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6036476	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6036478	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6048920	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes]
rs6048922	0.89[EUR][1000 genomes]
rs6048923	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[EUR][1000 genomes]
rs6048924	0.89[EUR][1000 genomes]
rs6048925	0.89[EUR][1000 genomes]
rs6048926	0.89[EUR][1000 genomes]
rs6048928	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6048929	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6048930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6048933	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6048936	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6048939	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6048941	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6048945	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6048946	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6048949	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6048950	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6048952	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6048956	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61035931	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6106685	0.89[EUR][1000 genomes]
rs6114201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6114206	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6114208	0.86[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6114209	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6515375	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67567111	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67997662	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71334202	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7265178	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7270413	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73318135	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs734801	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8114619	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8115417	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8115423	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8116859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8121147	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8121283	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8121405	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs911119	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.92[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
rs6036474	CST3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:74 , 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	chr20:23601800-23606000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr20:23601800-23606000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr20:23602000-23609400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr20:23602000-23610000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr20:23602000-23610200	Weak transcription	Lung	lung
7	chr20:23602000-23612200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr20:23602000-23616800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr20:23602400-23606600	Weak transcription	Gastric	stomach
10	chr20:23603000-23606400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr20:23603200-23604800	Enhancers	Fetal Intestine Small	intestine
12	chr20:23603200-23605400	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr20:23603600-23605000	Enhancers	K562	blood
14	chr20:23603800-23605800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr20:23603800-23606400	Weak transcription	Placenta	Placenta
16	chr20:23603800-23609200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr20:23603800-23609800	Weak transcription	Fetal Thymus	thymus
18	chr20:23603800-23615400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr20:23604000-23604600	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr20:23604000-23605000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr20:23604000-23605000	Enhancers	Adipose Nuclei	Adipose
22	chr20:23604000-23605000	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr20:23604000-23605000	Enhancers	Rectal Smooth Muscle	rectum
24	chr20:23604000-23605000	Enhancers	Stomach Mucosa	stomach
25	chr20:23604000-23605000	Weak transcription	GM12878-XiMat	blood
26	chr20:23604000-23606000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr20:23604000-23606600	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr20:23604000-23606600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr20:23604000-23606600	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr20:23604000-23606600	Weak transcription	Hela-S3	cervix
31	chr20:23604000-23607200	Enhancers	HepG2	liver
32	chr20:23604000-23607400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr20:23604000-23607400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr20:23604000-23608800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr20:23604000-23608800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr20:23604000-23609600	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr20:23604000-23610200	Weak transcription	Ovary	ovary
38	chr20:23604000-23612200	Weak transcription	Liver	Liver
39	chr20:23604000-23612800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr20:23604000-23613000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr20:23604000-23613000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr20:23604000-23613400	Weak transcription	Brain Hippocampus Middle	brain
43	chr20:23604000-23614400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr20:23604000-23616600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr20:23604000-23616800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr20:23604200-23604600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr20:23604200-23604600	Weak transcription	Aorta	Aorta
48	chr20:23604200-23604600	Weak transcription	Fetal Intestine Large	intestine
49	chr20:23604200-23604600	Weak transcription	Left Ventricle	heart
50	chr20:23604200-23604600	Weak transcription	Stomach Smooth Muscle	stomach

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