Variant report

Variant	rs487607
Chromosome Location	chr6:13415828-13415829
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:13396704..13399515-chr6:13413657..13416189,2	K562	blood:
2	chr6:13415611..13418241-chr6:13485753..13488399,3	MCF-7	breast:

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

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10807437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11753720	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11754291	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11758233	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1345031	0.81[ASN][1000 genomes]
rs1345032	0.82[ASN][1000 genomes]
rs1837701	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2119483	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2327673	0.94[EUR][1000 genomes]
rs4145562	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs478630	0.90[CHB][hapmap]
rs478804	0.91[CHB][hapmap]
rs480648	0.91[CHB][hapmap]
rs485804	0.91[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs490443	0.82[ASN][1000 genomes]
rs494026	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs500197	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs500293	0.91[CHB][hapmap]
rs519890	0.91[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs523221	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs536916	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs536998	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs550403	0.81[ASN][1000 genomes]
rs564361	0.89[CHB][hapmap];0.81[JPT][hapmap]
rs565013	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62385763	0.90[EUR][1000 genomes]
rs62386725	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62386727	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7742086	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9296672	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs935061	0.90[EUR][1000 genomes]
rs9357720	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9463764	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs9474117	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.83[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:67 , 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	chr6:13405000-13418400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr6:13405000-13421800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:13408600-13422600	Weak transcription	HSMM	muscle
5	chr6:13408800-13419400	Weak transcription	Primary B cells from cord blood	blood
6	chr6:13408800-13420200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr6:13408800-13423000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:13410400-13416000	Enhancers	Brain Cingulate Gyrus	brain
9	chr6:13410400-13416400	Enhancers	Right Atrium	heart
10	chr6:13410800-13416000	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr6:13411400-13416200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr6:13411400-13419600	Weak transcription	Fetal Thymus	thymus
13	chr6:13411400-13421800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:13411600-13424200	Enhancers	Right Ventricle	heart
15	chr6:13412200-13419000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:13412800-13416800	Enhancers	Brain Substantia Nigra	brain
17	chr6:13413200-13417800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr6:13413600-13419400	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr6:13413600-13419800	Weak transcription	Esophagus	oesophagus
20	chr6:13413800-13417800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr6:13413800-13419600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr6:13414000-13420000	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr6:13414000-13421400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr6:13414000-13421800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr6:13414000-13421800	Weak transcription	Brain Germinal Matrix	brain
26	chr6:13414000-13422000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr6:13414200-13416000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr6:13414200-13417800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr6:13414400-13416000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:13414600-13422000	Weak transcription	NHLF	lung
31	chr6:13414800-13419200	Weak transcription	Fetal Brain Female	brain
32	chr6:13414800-13420200	Weak transcription	HSMMtube	muscle
33	chr6:13415000-13416600	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr6:13415000-13417000	Weak transcription	Brain Anterior Caudate	brain
35	chr6:13415000-13417800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr6:13415000-13418600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr6:13415000-13419000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr6:13415000-13419200	Weak transcription	NHEK	skin
39	chr6:13415000-13420000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr6:13415000-13420400	Weak transcription	Colon Smooth Muscle	Colon
41	chr6:13415200-13417800	Weak transcription	Adipose Nuclei	Adipose
42	chr6:13415200-13418800	Weak transcription	Fetal Brain Male	brain
43	chr6:13415200-13419400	Enhancers	Stomach Smooth Muscle	stomach
44	chr6:13415200-13419600	Weak transcription	Primary T cells from cord blood	blood
45	chr6:13415200-13420200	Weak transcription	Rectal Smooth Muscle	rectum
46	chr6:13415400-13416000	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr6:13415400-13417000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr6:13415400-13417200	Weak transcription	Brain Angular Gyrus	brain
49	chr6:13415400-13417600	Weak transcription	Brain Hippocampus Middle	brain
50	chr6:13415400-13419000	Weak transcription	Fetal Muscle Leg	muscle

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