Variant report

Variant	rs34760929
Chromosome Location	chr6:128813659-128813660
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HDAC2	chr6:128813564-128814043	MCF-7	breast:	n/a	n/a
2	EP300	chr6:128813377-128814050	A549	lung:	n/a	n/a
3	FOXA1	chr6:128813659-128813853	T-47D	breast:	n/a	n/a
4	GATA3	chr6:128813648-128813913	T-47D	breast:	n/a	n/a
5	FOSL2	chr6:128813444-128813886	MCF-7	breast:	n/a	n/a
6	FOXA2	chr6:128813568-128813934	A549	lung:	n/a	n/a
7	FOS	chr6:128813641-128813797	MCF10A-Er-Src	breast:	n/a	n/a
8	FOXA1	chr6:128813547-128813862	T-47D	breast:	n/a	n/a
9	REST	chr6:128813494-128813881	A549	lung:	n/a	n/a
10	FOXA2	chr6:128813419-128813971	A549	lung:	n/a	n/a
11	GATA3	chr6:128813452-128814076	MCF-7	breast:	n/a	n/a
12	FOS	chr6:128813641-128813841	MCF10A-Er-Src	breast:	n/a	n/a
13	TCF12	chr6:128813294-128814098	A549	lung:	n/a	chr6:128814080-128814089
14	SP1	chr6:128813502-128814054	A549	lung:	n/a	n/a
15	FOSL2	chr6:128813366-128814009	A549	lung:	n/a	n/a
16	GATA3	chr6:128813232-128814229	MCF-7	breast:	n/a	n/a
17	GATA3	chr6:128813405-128814040	A549	lung:	n/a	n/a
18	FOS	chr6:128813641-128813816	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:128813517..128817980-chr6:128840263..128842508,4	MCF-7	breast:
2	chr6:128810906..128814817-chr6:128838628..128842024,3	MCF-7	breast:

No data

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	0.97[AFR][1000 genomes]
rs13196790	0.99[AFR][1000 genomes]
rs13201242	0.94[AFR][1000 genomes]
rs13216847	0.97[AFR][1000 genomes]
rs28360647	0.96[AFR][1000 genomes]
rs28550449	0.97[AFR][1000 genomes]
rs28705340	0.96[AFR][1000 genomes]
rs34337200	0.94[AFR][1000 genomes]
rs34558551	0.91[AFR][1000 genomes]
rs34931647	0.96[AFR][1000 genomes]
rs35242805	0.94[AFR][1000 genomes]
rs35395689	0.97[AFR][1000 genomes]
rs35419289	0.94[AFR][1000 genomes]
rs36120502	0.97[AFR][1000 genomes]
rs58050191	0.99[AFR][1000 genomes]
rs71568906	0.97[AFR][1000 genomes]
rs7760626	0.99[AFR][1000 genomes]
rs9482888	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs9482890	0.96[AFR][1000 genomes]
rs9491966	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9491967	0.99[AFR][1000 genomes]
rs9491970	0.99[AFR][1000 genomes]
rs9491972	0.99[AFR][1000 genomes]
rs9491975	0.96[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:83 , 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	chr6:128811400-128813800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:128811600-128814000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr6:128811800-128816600	Weak transcription	Gastric	stomach
7	chr6:128812000-128814200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr6:128812000-128814200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:128812000-128817000	Genic enhancers	HepG2	liver
10	chr6:128812200-128814000	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr6:128812200-128814200	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr6:128812200-128815000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:128812200-128817200	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr6:128812400-128814200	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr6:128812800-128813800	Active TSS	Stomach Smooth Muscle	stomach
16	chr6:128812800-128819400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr6:128813000-128814200	Enhancers	Fetal Intestine Large	intestine
18	chr6:128813000-128815000	Weak transcription	Fetal Thymus	thymus
19	chr6:128813000-128817800	Enhancers	Stomach Mucosa	stomach
20	chr6:128813000-128828600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr6:128813200-128814200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr6:128813200-128814200	Enhancers	Fetal Brain Female	brain
23	chr6:128813200-128814200	Enhancers	Fetal Stomach	stomach
24	chr6:128813200-128814200	Enhancers	Pancreas	Pancrea
25	chr6:128813200-128814200	Flanking Active TSS	A549	lung
26	chr6:128813200-128815000	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr6:128813200-128815200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:128813200-128819200	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr6:128813200-128820400	Weak transcription	Fetal Kidney	kidney
30	chr6:128813400-128814000	Weak transcription	Right Ventricle	heart
31	chr6:128813400-128814000	Enhancers	NHDF-Ad	bronchial
32	chr6:128813400-128814200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr6:128813400-128814200	Enhancers	Liver	Liver
34	chr6:128813400-128814200	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr6:128813400-128814200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr6:128813400-128814200	Enhancers	Right Atrium	heart
37	chr6:128813400-128814200	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr6:128813400-128814200	Enhancers	HUVEC	blood vessel
39	chr6:128813400-128814800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr6:128813400-128814800	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr6:128813400-128814800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr6:128813400-128815000	Enhancers	NHLF	lung
43	chr6:128813400-128815400	Enhancers	Brain Substantia Nigra	brain
44	chr6:128813400-128815800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr6:128813400-128816800	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr6:128813400-128816800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr6:128813400-128816800	Weak transcription	Left Ventricle	heart
48	chr6:128813400-128817600	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr6:128813400-128819200	Weak transcription	Colonic Mucosa	Colon
50	chr6:128813400-128819200	Weak transcription	Fetal Brain Male	brain

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