Variant report

Variant	rs9491972
Chromosome Location	chr6:128820063-128820064
allele	G/T
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	FOXA2	chr6:128819400-128820800	HepG2	liver:	n/a	chr6:128820296-128820308 chr6:128819464-128819476
2	SP1	chr6:128820050-128820942	HepG2	liver:	n/a	n/a
3	EP300	chr6:128819992-128820954	HepG2	liver:	n/a	n/a
4	FOXA1	chr6:128819992-128820965	HepG2	liver:	n/a	chr6:128820296-128820308
5	MYBL2	chr6:128819946-128821191	HepG2	liver:	n/a	n/a
6	ARID3A	chr6:128819996-128821599	HepG2	liver:	n/a	n/a
7	FOXA1	chr6:128819881-128820920	HepG2	liver:	n/a	chr6:128820296-128820308
8	NFIC	chr6:128819836-128821251	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:128819294..128822394-chr6:128840492..128843286,6	MCF-7	breast:
2	chr6:128818473..128821360-chr6:128825336..128827931,3	MCF-7	breast:
3	chr6:128813711..128816701-chr6:128817827..128820787,3	MCF-7	breast:
4	chr6:128817983..128822479-chr6:128839649..128843314,6	MCF-7	breast:

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

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

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10155795	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12717181	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13196790	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13201242	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13216847	1.00[CEU][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1341597	1.00[CEU][hapmap]
rs1341599	0.96[EUR][1000 genomes]
rs1891150	1.00[CEU][hapmap]
rs28360647	0.97[AFR][1000 genomes]
rs28550449	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28705340	0.97[AFR][1000 genomes]
rs34337200	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34558551	0.90[AFR][1000 genomes]
rs34760929	0.99[AFR][1000 genomes]
rs34931647	0.97[AFR][1000 genomes]
rs35242805	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35395689	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35419289	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36120502	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58050191	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61143917	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs71568904	0.96[EUR][1000 genomes]
rs71568905	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71568906	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7760626	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9482888	0.92[YRI][hapmap];0.96[AFR][1000 genomes]
rs9482890	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs9491951	1.00[CEU][hapmap]
rs9491964	0.96[EUR][1000 genomes]
rs9491967	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9491970	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9491971	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9491975	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:72 , 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	chr6:128813200-128820400	Weak transcription	Fetal Kidney	kidney
5	chr6:128813400-128825400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr6:128813600-128820400	Weak transcription	HSMM	muscle
7	chr6:128814000-128825200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr6:128814200-128821200	Weak transcription	Osteobl	bone
9	chr6:128814200-128821800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:128814200-128822200	Weak transcription	Fetal Stomach	stomach
11	chr6:128814200-128824800	Weak transcription	Right Ventricle	heart
12	chr6:128815000-128820400	Weak transcription	NHEK	skin
13	chr6:128815000-128821200	Weak transcription	NHLF	lung
14	chr6:128815200-128833800	Enhancers	Fetal Intestine Large	intestine
15	chr6:128815600-128822600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr6:128815800-128822800	Weak transcription	Fetal Thymus	thymus
17	chr6:128816400-128825600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:128816600-128820400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr6:128816800-128826600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:128817000-128820200	Enhancers	HepG2	liver
21	chr6:128817200-128820600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr6:128817200-128822000	Weak transcription	Left Ventricle	heart
23	chr6:128817200-128828600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr6:128817200-128839800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:128817200-128839800	Weak transcription	Aorta	Aorta
26	chr6:128818200-128820200	Enhancers	A549	lung
27	chr6:128818600-128820600	Enhancers	HUVEC	blood vessel
28	chr6:128818800-128821800	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr6:128818800-128822000	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr6:128819000-128820400	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr6:128819000-128820600	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr6:128819000-128822400	Enhancers	Fetal Heart	heart
33	chr6:128819200-128820200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr6:128819200-128820400	Enhancers	Rectal Smooth Muscle	rectum
35	chr6:128819200-128821200	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr6:128819200-128821800	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr6:128819200-128823400	Enhancers	Fetal Lung	lung
38	chr6:128819600-128820600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr6:128819600-128820800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr6:128819600-128820800	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr6:128819600-128821200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr6:128819600-128821200	Weak transcription	NH-A	brain
43	chr6:128819600-128821400	Weak transcription	Stomach Smooth Muscle	stomach
44	chr6:128819600-128821600	Enhancers	Brain Substantia Nigra	brain
45	chr6:128819600-128824000	Weak transcription	Pancreas	Pancrea
46	chr6:128819600-128824600	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr6:128819600-128825200	Weak transcription	Colon Smooth Muscle	Colon
48	chr6:128819600-128827600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr6:128819800-128820200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
50	chr6:128819800-128820200	Weak transcription	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links