Variant report

Variant	rs1550520
Chromosome Location	chr6:13428041-13428042
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	chr6:13426005..13428428-chr6:13430205..13432759,2	K562	blood:
2	chr6:13426718..13428428-chr6:13429369..13431705,2	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1345031	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1345032	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1550521	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2119481	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2119482	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2119484	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2165419	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4145562	0.87[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs4454121	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4715251	0.83[CEU][hapmap]
rs4715261	0.83[EUR][1000 genomes]
rs476138	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs478630	0.90[CEU][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs478804	0.90[CEU][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs480648	0.90[CEU][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs485804	0.91[CEU][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs490443	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs500197	0.91[CEU][hapmap]
rs500293	0.90[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs503117	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs508153	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs519657	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs519890	0.90[CEU][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs536916	0.91[CEU][hapmap]
rs536998	0.90[CEU][hapmap]
rs550403	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs558126	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs558242	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs559565	0.84[CEU][hapmap]
rs559612	0.90[CEU][hapmap]
rs563424	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs564361	0.88[CEU][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs566320	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62385763	0.85[ASN][1000 genomes]
rs6458814	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6458815	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6910652	0.95[CEU][hapmap];0.94[CHB][hapmap];0.96[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs821299	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9296672	0.87[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs935061	0.85[ASN][1000 genomes]
rs9357727	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9370104	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9395768	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9395770	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9463764	0.87[CHB][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1033620	chr6:13419730-13571788	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv462640	chr6:13426539-13519434	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv600994	chr6:13426539-13519434	Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13419200-13428200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr6:13419400-13429800	Enhancers	Fetal Lung	lung
3	chr6:13420200-13430000	Enhancers	Fetal Stomach	stomach
4	chr6:13422000-13428600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr6:13422200-13432800	Weak transcription	NHDF-Ad	bronchial
6	chr6:13423400-13428200	Weak transcription	K562	blood
7	chr6:13423400-13428800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr6:13423400-13428800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:13423400-13432200	Weak transcription	A549	lung
10	chr6:13423800-13428800	Weak transcription	Fetal Brain Female	brain
11	chr6:13423800-13431400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr6:13423800-13431400	Weak transcription	Brain Germinal Matrix	brain
13	chr6:13423800-13433000	Weak transcription	Pancreas	Pancrea
14	chr6:13424000-13428200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr6:13424000-13428400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr6:13424000-13428800	Enhancers	Stomach Smooth Muscle	stomach
17	chr6:13424000-13429000	Weak transcription	Aorta	Aorta
18	chr6:13424000-13429200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr6:13424200-13428200	Weak transcription	HUVEC	blood vessel
20	chr6:13425200-13429600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr6:13425200-13430000	Enhancers	Lung	lung
22	chr6:13425200-13430200	Enhancers	Primary B cells from peripheral blood	blood
23	chr6:13425200-13431200	Enhancers	Left Ventricle	heart
24	chr6:13425200-13432200	Enhancers	Right Ventricle	heart
25	chr6:13425400-13428200	Enhancers	Adipose Nuclei	Adipose
26	chr6:13425400-13428400	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr6:13425400-13430200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr6:13425800-13428600	Weak transcription	Small Intestine	intestine
29	chr6:13425800-13429800	Enhancers	H1 Cell Line	embryonic stem cell
30	chr6:13426000-13428200	Weak transcription	Fetal Kidney	kidney
31	chr6:13426000-13428600	Weak transcription	Colonic Mucosa	Colon
32	chr6:13426000-13429800	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr6:13426000-13430400	Flanking Active TSS	GM12878-XiMat	blood
34	chr6:13426200-13430000	Enhancers	Fetal Thymus	thymus
35	chr6:13426400-13429800	Enhancers	Fetal Heart	heart
36	chr6:13426600-13428200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr6:13426600-13428400	Weak transcription	Rectal Smooth Muscle	rectum
38	chr6:13426600-13429600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:13426600-13431200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr6:13426800-13428200	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr6:13426800-13428400	Weak transcription	Brain Anterior Caudate	brain
42	chr6:13426800-13428800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr6:13426800-13429200	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr6:13426800-13429400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr6:13426800-13429400	Weak transcription	NHEK	skin
46	chr6:13426800-13431600	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr6:13426800-13431600	Weak transcription	NHLF	lung
48	chr6:13426800-13431800	Weak transcription	NH-A	brain
49	chr6:13427000-13428200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr6:13427000-13428200	Weak transcription	Brain Cingulate Gyrus	brain

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