Variant report

Variant	rs200220
Chromosome Location	chr13:50960378-50960379
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	chr13:50697837..50700785-chr13:50959097..50961406,2	K562	blood:

Variant related genes	Relation type
ENSG00000231607	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1262871	0.92[ASN][1000 genomes]
rs149874	0.92[ASN][1000 genomes]
rs183911	0.92[ASN][1000 genomes]
rs188014	0.93[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200219	0.85[CEU][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200225	0.92[ASN][1000 genomes]
rs201797	0.92[ASN][1000 genomes]
rs201799	0.92[ASN][1000 genomes]
rs201800	0.92[ASN][1000 genomes]
rs201803	0.93[ASW][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.92[ASN][1000 genomes]
rs2532974	0.92[ASN][1000 genomes]
rs2812218	0.92[ASN][1000 genomes]
rs2812219	0.92[ASN][1000 genomes]
rs988872	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2752608	chr13:50550099-51054499	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1249 gene(s)	inside rSNPs	diseases
5	nsv832609	chr13:50946577-51065968	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50950400-50967200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr13:50951600-50961000	Weak transcription	Pancreas	Pancrea
3	chr13:50955600-50960400	Weak transcription	HepG2	liver
4	chr13:50956200-50960800	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr13:50956600-50961000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr13:50957400-50960600	Weak transcription	Right Ventricle	heart
7	chr13:50958600-50961800	Enhancers	Thymus	Thymus
8	chr13:50958600-50961800	Enhancers	Dnd41	blood
9	chr13:50958600-50962800	Enhancers	Fetal Thymus	thymus
10	chr13:50958800-50960800	Enhancers	Psoas Muscle	Psoas
11	chr13:50959000-50960800	Enhancers	HSMM	muscle
12	chr13:50959000-50961800	Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr13:50959200-50960400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr13:50959600-50960400	Enhancers	Brain Anterior Caudate	brain
15	chr13:50959600-50960400	Enhancers	Fetal Muscle Leg	muscle
16	chr13:50959600-50960800	Enhancers	Brain Cingulate Gyrus	brain
17	chr13:50959800-50960600	Enhancers	Brain Hippocampus Middle	brain
18	chr13:50959800-50960600	Enhancers	Brain Substantia Nigra	brain
19	chr13:50959800-50960800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr13:50959800-50960800	Enhancers	Fetal Lung	lung
21	chr13:50959800-50961000	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr13:50959800-50961000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr13:50959800-50961000	Flanking Active TSS	Liver	Liver
24	chr13:50959800-50961800	Enhancers	Fetal Kidney	kidney
25	chr13:50959800-50961800	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr13:50959800-50962600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr13:50959800-50963000	Enhancers	H1 Cell Line	embryonic stem cell
28	chr13:50960000-50960400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr13:50960000-50960600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr13:50960000-50960600	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr13:50960000-50961000	Enhancers	Muscle Satellite Cultured Cells	--
32	chr13:50960000-50961000	Active TSS	Fetal Muscle Trunk	muscle
33	chr13:50960000-50961600	Enhancers	Brain Angular Gyrus	brain
34	chr13:50960000-50961600	Enhancers	Fetal Stomach	stomach
35	chr13:50960000-50961600	Flanking Active TSS	HSMMtube	muscle
36	chr13:50960000-50961800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr13:50960000-50965000	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr13:50960200-50960600	Enhancers	Colon Smooth Muscle	Colon
39	chr13:50960200-50960800	Weak transcription	Aorta	Aorta
40	chr13:50960200-50960800	Weak transcription	Left Ventricle	heart
41	chr13:50960200-50960800	Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr13:50960200-50961200	Flanking Active TSS	Fetal Heart	heart
43	chr13:50960200-50961400	Enhancers	NH-A	brain
44	chr13:50960200-50961800	Enhancers	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links