Variant report

Variant	rs9482888
Chromosome Location	chr6:128814111-128814112
allele	C/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	GATA3	chr6:128813232-128814229	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:128811185..128813602-chr6:128813721..128815755,2	MCF-7	breast:
2	chr6:128813517..128817980-chr6:128840263..128842508,4	MCF-7	breast:
3	chr6:128813711..128816701-chr6:128817827..128820787,3	MCF-7	breast:
4	chr6:128810906..128814817-chr6:128838628..128842024,3	MCF-7	breast:

Variant related genes	Relation type
PTPRK	TF binding region
ENSG00000152894	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10155795	0.91[YRI][hapmap];0.94[AFR][1000 genomes]
rs13196790	0.95[YRI][hapmap];0.96[AFR][1000 genomes]
rs13201242	0.91[AFR][1000 genomes]
rs13216847	0.88[YRI][hapmap];0.94[AFR][1000 genomes]
rs28360647	0.93[AFR][1000 genomes]
rs28550449	0.94[AFR][1000 genomes]
rs28705340	0.93[AFR][1000 genomes]
rs34337200	0.92[AFR][1000 genomes]
rs34558551	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34760929	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs34931647	0.93[AFR][1000 genomes]
rs35242805	0.92[AFR][1000 genomes]
rs35395689	0.94[AFR][1000 genomes]
rs35419289	0.91[AFR][1000 genomes]
rs36120502	0.94[AFR][1000 genomes]
rs58050191	0.96[AFR][1000 genomes]
rs71568906	0.94[AFR][1000 genomes]
rs7760626	0.96[AFR][1000 genomes]
rs9482890	0.91[YRI][hapmap];0.93[AFR][1000 genomes]
rs9491966	0.83[AMR][1000 genomes]
rs9491967	0.92[YRI][hapmap];0.96[AFR][1000 genomes]
rs9491970	0.92[YRI][hapmap];0.96[AFR][1000 genomes]
rs9491972	0.92[YRI][hapmap];0.96[AFR][1000 genomes]
rs9491975	0.92[YRI][hapmap];0.93[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:81 , 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	chr6:128811000-128814400	Enhancers	Small Intestine	intestine
4	chr6:128811800-128816600	Weak transcription	Gastric	stomach
5	chr6:128812000-128814200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr6:128812000-128814200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:128812000-128817000	Genic enhancers	HepG2	liver
8	chr6:128812200-128814200	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr6:128812200-128815000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:128812200-128817200	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr6:128812400-128814200	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr6:128812800-128819400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:128813000-128814200	Enhancers	Fetal Intestine Large	intestine
14	chr6:128813000-128815000	Weak transcription	Fetal Thymus	thymus
15	chr6:128813000-128817800	Enhancers	Stomach Mucosa	stomach
16	chr6:128813000-128828600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:128813200-128814200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:128813200-128814200	Enhancers	Fetal Brain Female	brain
19	chr6:128813200-128814200	Enhancers	Fetal Stomach	stomach
20	chr6:128813200-128814200	Enhancers	Pancreas	Pancrea
21	chr6:128813200-128814200	Flanking Active TSS	A549	lung
22	chr6:128813200-128815000	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr6:128813200-128815200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:128813200-128819200	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr6:128813200-128820400	Weak transcription	Fetal Kidney	kidney
26	chr6:128813400-128814200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr6:128813400-128814200	Enhancers	Liver	Liver
28	chr6:128813400-128814200	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr6:128813400-128814200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr6:128813400-128814200	Enhancers	Right Atrium	heart
31	chr6:128813400-128814200	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr6:128813400-128814200	Enhancers	HUVEC	blood vessel
33	chr6:128813400-128814800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr6:128813400-128814800	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr6:128813400-128814800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr6:128813400-128815000	Enhancers	NHLF	lung
37	chr6:128813400-128815400	Enhancers	Brain Substantia Nigra	brain
38	chr6:128813400-128815800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr6:128813400-128816800	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr6:128813400-128816800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr6:128813400-128816800	Weak transcription	Left Ventricle	heart
42	chr6:128813400-128817600	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr6:128813400-128819200	Weak transcription	Colonic Mucosa	Colon
44	chr6:128813400-128819200	Weak transcription	Fetal Brain Male	brain
45	chr6:128813400-128819400	Weak transcription	Psoas Muscle	Psoas
46	chr6:128813400-128820000	Enhancers	Fetal Intestine Small	intestine
47	chr6:128813400-128820000	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr6:128813400-128825400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr6:128813600-128814200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr6:128813600-128814200	Enhancers	Muscle Satellite Cultured Cells	--

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