Variant report

Variant	rs6036478
Chromosome Location	chr20:23611359-23611360
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:23610507..23612555-chr20:23613561..23616038,2	MCF-7	breast:
2	chr20:23610829..23612765-chr20:23625069..23626806,2	MCF-7	breast:
3	chr20:23593307..23595143-chr20:23609634..23612477,2	K562	blood:
4	chr20:23608610..23615599-chr20:23616056..23619619,19	MCF-7	breast:
5	chr20:23563903..23566418-chr20:23609795..23611808,3	MCF-7	breast:
6	chr20:23606151..23608595-chr20:23610355..23612719,2	K562	blood:
7	chr20:23603350..23604972-chr20:23610943..23612814,2	K562	blood:
8	chr20:23339592..23341756-chr20:23608896..23611631,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000101439	Chromatin interaction
ENSG00000204658	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	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1011226	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1064039	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1158167	0.89[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs12624424	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12625182	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12625716	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12710327	0.82[EUR][1000 genomes]
rs13037490	0.85[CEU][hapmap];0.88[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs13038305	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13038337	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13038990	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13039536	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]
rs13041070	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13043266	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13043610	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1555355	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17751897	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2016161	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2067488	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2208289	0.86[EUR][1000 genomes]
rs2254635	0.84[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2405367	0.85[CEU][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2405392	0.90[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.81[EUR][1000 genomes]
rs2405393	0.81[EUR][1000 genomes]
rs2424582	0.85[CEU][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28703706	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3004139	0.86[EUR][1000 genomes]
rs3004145	0.86[EUR][1000 genomes]
rs3088162	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34374560	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34746357	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34792920	0.81[EUR][1000 genomes]
rs34897231	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34911568	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35488434	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35573837	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35610040	0.90[CEU][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35782710	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35966482	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3761280	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3761281	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3787498	0.90[CEU][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3787499	0.90[CEU][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3810575	0.90[CEU][hapmap];0.88[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs3827141	0.90[CEU][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3827142	0.90[CEU][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3827143	0.90[CEU][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4346460	0.90[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs4815222	0.90[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs4815223	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs4815224	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5030707	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55897275	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56371840	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56388902	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57549987	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59059917	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6036461	0.90[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs6036463	0.86[EUR][1000 genomes]
rs6036465	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6036469	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6036470	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6036471	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6036474	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6036476	0.81[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6048920	0.90[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs6048922	0.86[EUR][1000 genomes]
rs6048923	0.85[CEU][hapmap];0.88[CHB][hapmap];0.88[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	0.85[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6048929	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6048930	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6048933	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6048936	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6048939	0.83[EUR][1000 genomes]
rs6048941	0.83[EUR][1000 genomes]
rs6048945	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6048946	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6048949	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6048950	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6048952	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6048956	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61035931	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6106685	0.85[EUR][1000 genomes]
rs6114201	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6114206	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6114208	0.85[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6114209	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6515375	0.84[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67567111	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67997662	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71334202	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7265178	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7270413	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73318135	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs734801	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8114619	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8115417	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8115423	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8116859	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8121147	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8121283	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8121405	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs911119	0.94[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[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
rs6036478	CST3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:98 , 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	chr20:23602000-23612200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr20:23602000-23616800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr20:23603800-23615400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr20:23604000-23612200	Weak transcription	Liver	Liver
6	chr20:23604000-23612800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr20:23604000-23613000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr20:23604000-23613000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr20:23604000-23613400	Weak transcription	Brain Hippocampus Middle	brain
10	chr20:23604000-23614400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr20:23604000-23616600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr20:23604000-23616800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr20:23604200-23615000	Weak transcription	Brain Anterior Caudate	brain
14	chr20:23604800-23612200	Weak transcription	Aorta	Aorta
15	chr20:23605000-23611800	Weak transcription	Fetal Muscle Leg	muscle
16	chr20:23605000-23612800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr20:23605200-23612200	Weak transcription	NHLF	lung
18	chr20:23605400-23612200	Weak transcription	Stomach Smooth Muscle	stomach
19	chr20:23606600-23615200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr20:23606600-23617000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr20:23606800-23616600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr20:23607000-23612600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr20:23607000-23615000	Weak transcription	Colon Smooth Muscle	Colon
24	chr20:23607200-23612800	Weak transcription	Gastric	stomach
25	chr20:23607400-23612600	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr20:23607400-23612600	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr20:23607600-23612600	Weak transcription	Pancreas	Pancrea
28	chr20:23607600-23615400	Weak transcription	Fetal Kidney	kidney
29	chr20:23608000-23612400	Weak transcription	Fetal Stomach	stomach
30	chr20:23608200-23614400	Weak transcription	Thymus	Thymus
31	chr20:23608800-23611400	Enhancers	Left Ventricle	heart
32	chr20:23608800-23611400	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr20:23608800-23611400	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr20:23608800-23613400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr20:23609000-23611400	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr20:23609000-23611400	Enhancers	Spleen	Spleen
37	chr20:23609200-23611400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr20:23609200-23611400	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr20:23609200-23611400	Enhancers	HUVEC	blood vessel
40	chr20:23609600-23611400	Enhancers	Rectal Mucosa Donor 29	rectum
41	chr20:23609600-23612000	Weak transcription	Brain Germinal Matrix	brain
42	chr20:23609600-23612600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr20:23609600-23615000	Weak transcription	HSMMtube	muscle
44	chr20:23609800-23612000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr20:23609800-23616800	Weak transcription	Primary hematopoietic stem cells	blood
46	chr20:23610000-23613800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr20:23610200-23611400	Enhancers	Lung	lung
48	chr20:23610200-23611400	Enhancers	Ovary	ovary
49	chr20:23610200-23612000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr20:23610200-23616800	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links