Variant report

Variant	rs705601
Chromosome Location	chr6:101314005-101314006
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	chr6:101311227..101314088-chr6:101316060..101317818,2	MCF-7	breast:
2	chr6:101309650..101312548-chr6:101313030..101314755,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11155726	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12189857	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17061209	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17061230	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17673031	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2749130	1.00[ASN][1000 genomes]
rs2756040	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4839795	1.00[ASN][1000 genomes]
rs592463	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs600653	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs601360	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs606032	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs609522	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs612117	1.00[ASN][1000 genomes]
rs612459	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs613338	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs614097	1.00[ASN][1000 genomes]
rs617365	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs625745	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs626411	1.00[ASN][1000 genomes]
rs635258	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs640315	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs648360	0.83[EUR][1000 genomes]
rs668932	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs673138	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs674589	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705594	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705595	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705598	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705602	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705609	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705612	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705618	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs705619	0.82[EUR][1000 genomes]
rs72944877	1.00[ASN][1000 genomes]
rs72946427	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72947091	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72951137	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72951161	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7755696	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs817226	1.00[ASN][1000 genomes]
rs817227	1.00[ASN][1000 genomes]
rs817234	1.00[ASN][1000 genomes]
rs846784	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs846790	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs846796	0.83[EUR][1000 genomes]
rs861752	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949535	chr6:100740293-101469052	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1020692	chr6:101136992-101426071	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv886457	chr6:101158950-101487473	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1020400	chr6:101172705-101981665	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv538390	chr6:101172705-101981665	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv1019213	chr6:101225650-101623140	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv538391	chr6:101225650-101623140	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	esv2763587	chr6:101277874-101510491	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs705601	ASCC3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:101269200-101326600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:101275800-101314400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr6:101281200-101317000	Weak transcription	Small Intestine	intestine
4	chr6:101285600-101326600	Weak transcription	NHLF	lung
5	chr6:101290200-101318200	Weak transcription	Fetal Lung	lung
6	chr6:101291200-101326400	Weak transcription	Brain Anterior Caudate	brain
7	chr6:101294000-101320400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:101294200-101314200	Weak transcription	Colon Smooth Muscle	Colon
9	chr6:101294600-101314400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr6:101294600-101320600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr6:101294600-101325400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr6:101294600-101328600	Weak transcription	Spleen	Spleen
13	chr6:101294800-101325600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:101295000-101325800	Weak transcription	Brain Angular Gyrus	brain
15	chr6:101295000-101325800	Weak transcription	Stomach Smooth Muscle	stomach
16	chr6:101296000-101323400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr6:101296800-101317000	Weak transcription	HSMMtube	muscle
18	chr6:101296800-101323800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr6:101297000-101327200	Weak transcription	Fetal Muscle Leg	muscle
20	chr6:101297000-101328200	Weak transcription	Ovary	ovary
21	chr6:101300200-101319000	Weak transcription	Fetal Stomach	stomach
22	chr6:101300200-101326600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:101300200-101328400	Weak transcription	Esophagus	oesophagus
24	chr6:101300200-101328400	Weak transcription	Lung	lung
25	chr6:101302600-101327800	Weak transcription	Stomach Mucosa	stomach
26	chr6:101303000-101314800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:101303200-101316000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr6:101303200-101316400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:101303200-101317200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr6:101303600-101321400	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr6:101303800-101316200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr6:101303800-101325600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr6:101304200-101326600	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr6:101304400-101327800	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr6:101304600-101317200	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr6:101304800-101314200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr6:101304800-101317200	Strong transcription	Dnd41	blood
38	chr6:101304800-101325400	Weak transcription	Brain Substantia Nigra	brain
39	chr6:101305000-101316200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr6:101305000-101327800	Weak transcription	Rectal Smooth Muscle	rectum
41	chr6:101305200-101314200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr6:101305200-101315600	Weak transcription	Brain Hippocampus Middle	brain
43	chr6:101305200-101316000	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr6:101305200-101316400	Strong transcription	Primary B cells from cord blood	blood
45	chr6:101305200-101316400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr6:101305200-101316400	Strong transcription	HSMM	muscle
47	chr6:101305200-101316600	Strong transcription	HMEC	breast
48	chr6:101305200-101317400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr6:101305600-101316000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr6:101305800-101314200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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