Variant report

Variant	rs558242
Chromosome Location	chr6:13407626-13407627
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13405977..13407729-chr6:13485216..13487161,3	MCF-7	breast:
2	chr6:13400278..13401808-chr6:13406310..13408265,2	MCF-7	breast:
3	chr6:13405420..13408218-chr6:13438666..13440547,2	K562	blood:
4	chr6:13406818..13408886-chr6:13483840..13488220,5	MCF-7	breast:
5	chr6:13406137..13408577-chr6:13573927..13576170,2	MCF-7	breast:
6	chr6:13406145..13408180-chr6:13453724..13455818,2	MCF-7	breast:
7	chr6:13395967..13397504-chr6:13405065..13407928,2	K562	blood:

Variant related genes	Relation type
ENSG00000187461	Chromatin interaction
ENSG00000124523	Chromatin interaction
ENSG00000145990	Chromatin interaction
ENSG00000237786	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1345031	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1345032	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1550520	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1550521	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2119481	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2119484	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2165419	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4454121	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4715251	0.94[ASN][1000 genomes]
rs4715261	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs476138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs478630	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs478804	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs480648	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs485804	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs488885	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs490443	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs494026	0.87[ASN][1000 genomes]
rs500197	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs500293	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs503117	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs508153	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs513613	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs519657	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs519890	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs520828	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs536916	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs536998	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs544639	0.82[EUR][1000 genomes]
rs546507	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs550403	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs558126	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs559565	0.92[ASN][1000 genomes]
rs559612	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs563424	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs563662	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs564361	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs566320	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62386724	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6458814	0.83[EUR][1000 genomes]
rs6458815	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6910652	0.83[EUR][1000 genomes]
rs7742086	0.87[ASN][1000 genomes]
rs821298	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs821299	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs821300	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9370104	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9395768	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9474117	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13401800-13419000	Weak transcription	Primary B cells from peripheral blood	blood
2	chr6:13403600-13409600	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr6:13404000-13408800	Enhancers	Brain Angular Gyrus	brain
4	chr6:13404000-13409000	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr6:13404400-13407800	Enhancers	NHLF	lung
6	chr6:13404400-13408200	Enhancers	Brain Cingulate Gyrus	brain
7	chr6:13404400-13408800	Enhancers	Adipose Nuclei	Adipose
8	chr6:13404400-13408800	Enhancers	Left Ventricle	heart
9	chr6:13404400-13408800	Enhancers	Psoas Muscle	Psoas
10	chr6:13404400-13408800	Enhancers	Right Atrium	heart
11	chr6:13404400-13409000	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr6:13404400-13411400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:13404800-13408600	Enhancers	Spleen	Spleen
14	chr6:13405000-13410200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr6:13405000-13418400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr6:13405000-13421800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr6:13405200-13408800	Enhancers	Brain Anterior Caudate	brain
18	chr6:13405400-13407800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:13405400-13409800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr6:13405400-13410400	Weak transcription	Aorta	Aorta
21	chr6:13405600-13408600	Enhancers	Fetal Muscle Leg	muscle
22	chr6:13406000-13408600	Enhancers	Duodenum Mucosa	Duodenum
23	chr6:13406000-13408800	Enhancers	Primary B cells from cord blood	blood
24	chr6:13406000-13408800	Enhancers	Lung	lung
25	chr6:13406000-13408800	Enhancers	Right Ventricle	heart
26	chr6:13406200-13407800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr6:13406200-13409000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr6:13406400-13408800	Flanking Active TSS	HepG2	liver
29	chr6:13406600-13407800	Flanking Active TSS	Brain Substantia Nigra	brain
30	chr6:13406600-13408000	Enhancers	Small Intestine	intestine
31	chr6:13406600-13408600	Enhancers	Colon Smooth Muscle	Colon
32	chr6:13406600-13408800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:13406600-13409000	Enhancers	Esophagus	oesophagus
34	chr6:13406800-13408800	Enhancers	Pancreatic Islets	Pancreatic Islet
35	chr6:13406800-13409000	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr6:13406800-13409000	Enhancers	HMEC	breast
37	chr6:13407000-13408000	Enhancers	HSMMtube	muscle
38	chr6:13407000-13408600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr6:13407000-13408600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr6:13407000-13408600	Enhancers	Fetal Lung	lung
41	chr6:13407000-13408600	Enhancers	Gastric	stomach
42	chr6:13407000-13408600	Enhancers	Pancreas	Pancrea
43	chr6:13407000-13408800	Strong transcription	GM12878-XiMat	blood
44	chr6:13407200-13408000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
45	chr6:13407200-13408200	Enhancers	Liver	Liver
46	chr6:13407200-13408600	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr6:13407200-13408600	Enhancers	Osteobl	bone
48	chr6:13407200-13408800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr6:13407200-13408800	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr6:13407200-13408800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links