Variant report

Variant	rs9491975
Chromosome Location	chr6:128821446-128821447
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr6:128821227-128821551	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr6:128821389-128821478	MCF10A-Er-Src	breast:	n/a	n/a
3	FOXA2	chr6:128821142-128821482	HepG2	liver:	n/a	n/a
4	ARID3A	chr6:128819996-128821599	HepG2	liver:	n/a	n/a
5	CEBPB	chr6:128821211-128821508	A549	lung:	n/a	n/a
6	STAT3	chr6:128821362-128821663	MCF10A-Er-Src	breast:	n/a	n/a
7	CEBPB	chr6:128821189-128821550	Hela-S3	cervix:	n/a	n/a
8	MYC	chr6:128821323-128821633	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr6:128821232-128821555	MCF10A-Er-Src	breast:	n/a	n/a
10	TCF12	chr6:128820378-128821608	A549	lung:	n/a	n/a
11	CEBPB	chr6:128821160-128821612	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:128819294..128822394-chr6:128840492..128843286,6	MCF-7	breast:
2	chr6:128817983..128822479-chr6:128839649..128843314,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224733	TF binding region
ENSG00000227112	TF binding region
ENSG00000152894	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10155795	1.00[YRI][hapmap];0.99[AFR][1000 genomes]
rs13196432	0.80[CEU][hapmap];0.86[EUR][1000 genomes]
rs13196790	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs13201242	0.96[AFR][1000 genomes]
rs13216847	0.96[YRI][hapmap];0.99[AFR][1000 genomes]
rs1341598	0.87[CEU][hapmap];0.95[EUR][1000 genomes]
rs28360647	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28550449	0.99[AFR][1000 genomes]
rs28705340	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34337200	0.96[AFR][1000 genomes]
rs34478800	0.95[EUR][1000 genomes]
rs34558551	0.87[AFR][1000 genomes]
rs34760929	0.96[AFR][1000 genomes]
rs34931647	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35242805	0.96[AFR][1000 genomes]
rs35395689	0.99[AFR][1000 genomes]
rs35419289	0.96[AFR][1000 genomes]
rs36120502	0.99[AFR][1000 genomes]
rs58050191	0.97[AFR][1000 genomes]
rs6937769	0.83[EUR][1000 genomes]
rs71568906	0.99[AFR][1000 genomes]
rs7760626	0.97[AFR][1000 genomes]
rs9482888	0.92[YRI][hapmap];0.93[AFR][1000 genomes]
rs9482890	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9491958	0.95[EUR][1000 genomes]
rs9491967	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs9491970	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs9491972	1.00[YRI][hapmap];0.97[AFR][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	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1020071	chr6:128579774-129048919	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv538441	chr6:128579774-129048919	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv830800	chr6:128710631-128878435	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128797400-128822000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:128808800-128830800	Weak transcription	Lung	lung
3	chr6:128813000-128828600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:128813400-128825400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:128814000-128825200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr6:128814200-128821800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:128814200-128822200	Weak transcription	Fetal Stomach	stomach
8	chr6:128814200-128824800	Weak transcription	Right Ventricle	heart
9	chr6:128815200-128833800	Enhancers	Fetal Intestine Large	intestine
10	chr6:128815600-128822600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr6:128815800-128822800	Weak transcription	Fetal Thymus	thymus
12	chr6:128816400-128825600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:128816800-128826600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:128817200-128822000	Weak transcription	Left Ventricle	heart
15	chr6:128817200-128828600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr6:128817200-128839800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:128817200-128839800	Weak transcription	Aorta	Aorta
18	chr6:128818800-128821800	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr6:128818800-128822000	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr6:128819000-128822400	Enhancers	Fetal Heart	heart
21	chr6:128819200-128821800	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr6:128819200-128823400	Enhancers	Fetal Lung	lung
23	chr6:128819600-128821600	Enhancers	Brain Substantia Nigra	brain
24	chr6:128819600-128824000	Weak transcription	Pancreas	Pancrea
25	chr6:128819600-128824600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr6:128819600-128825200	Weak transcription	Colon Smooth Muscle	Colon
27	chr6:128819600-128827600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr6:128819800-128821800	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr6:128819800-128822000	Weak transcription	Fetal Brain Male	brain
30	chr6:128819800-128824800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr6:128819800-128824800	Weak transcription	Ovary	ovary
32	chr6:128819800-128825200	Weak transcription	Small Intestine	intestine
33	chr6:128819800-128825400	Weak transcription	Psoas Muscle	Psoas
34	chr6:128819800-128825600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr6:128819800-128825600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr6:128819800-128825600	Weak transcription	Right Atrium	heart
37	chr6:128819800-128826600	Weak transcription	Brain Angular Gyrus	brain
38	chr6:128819800-128828600	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr6:128819800-128828600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr6:128820200-128822200	Enhancers	Stomach Mucosa	stomach
41	chr6:128820400-128821600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
42	chr6:128820400-128821800	Enhancers	Muscle Satellite Cultured Cells	--
43	chr6:128820400-128822800	Enhancers	NHEK	skin
44	chr6:128820400-128825600	Weak transcription	Rectal Smooth Muscle	rectum
45	chr6:128820600-128821800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr6:128820600-128822200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr6:128820600-128822600	Weak transcription	HUVEC	blood vessel
48	chr6:128820600-128822800	Enhancers	NHDF-Ad	bronchial
49	chr6:128820600-128826600	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr6:128820600-128833800	Enhancers	Fetal Intestine Small	intestine

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