Variant report

Variant	rs11756545
Chromosome Location	chr6:128813895-128813896
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 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	POLR2A	chr6:128813764-128814086	HepG2	liver:	n/a	n/a
3	EP300	chr6:128813377-128814050	A549	lung:	n/a	n/a
4	GATA3	chr6:128813648-128813913	T-47D	breast:	n/a	n/a
5	FOXA2	chr6:128813568-128813934	A549	lung:	n/a	n/a
6	FOXA2	chr6:128813419-128813971	A549	lung:	n/a	n/a
7	GATA3	chr6:128813452-128814076	MCF-7	breast:	n/a	n/a
8	TCF12	chr6:128813294-128814098	A549	lung:	n/a	chr6:128814080-128814089
9	SP1	chr6:128813502-128814054	A549	lung:	n/a	n/a
10	FOSL2	chr6:128813366-128814009	A549	lung:	n/a	n/a
11	GATA3	chr6:128813232-128814229	MCF-7	breast:	n/a	n/a
12	GATA3	chr6:128813405-128814040	A549	lung:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

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:

No data

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

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1012629	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs10872331	1.00[CHD][hapmap]
rs11154439	1.00[CHD][hapmap]
rs17364020	1.00[CHD][hapmap]
rs17364090	1.00[CHD][hapmap]
rs17364118	1.00[CHD][hapmap]
rs17459694	1.00[ASN][1000 genomes]
rs17460765	1.00[ASN][1000 genomes]
rs17460940	1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[ASN][1000 genomes]
rs17461178	1.00[ASN][1000 genomes]
rs17461290	1.00[CHD][hapmap]
rs17461370	1.00[CHD][hapmap]
rs1935130	1.00[ASN][1000 genomes]
rs2326702	1.00[CHD][hapmap]
rs62425728	1.00[ASN][1000 genomes]
rs62425730	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62425732	1.00[ASN][1000 genomes]
rs62425734	1.00[ASN][1000 genomes]
rs62425736	1.00[ASN][1000 genomes]
rs9482886	1.00[ASN][1000 genomes]
rs9491959	1.00[ASN][1000 genomes]
rs9492002	1.00[CHD][hapmap]
rs9492021	1.00[CHD][hapmap]

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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11756545	AKAP7	cis	parietal	SCAN
rs11756545	MOXD1	cis	parietal	SCAN

Chromatin state (count:82 , 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	chr6:128811600-128814000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr6:128811800-128816600	Weak transcription	Gastric	stomach
6	chr6:128812000-128814200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:128812000-128814200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:128812000-128817000	Genic enhancers	HepG2	liver
9	chr6:128812200-128814000	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr6:128812200-128814200	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr6:128812200-128815000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:128812200-128817200	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr6:128812400-128814200	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr6:128812800-128819400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr6:128813000-128814200	Enhancers	Fetal Intestine Large	intestine
16	chr6:128813000-128815000	Weak transcription	Fetal Thymus	thymus
17	chr6:128813000-128817800	Enhancers	Stomach Mucosa	stomach
18	chr6:128813000-128828600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:128813200-128814200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr6:128813200-128814200	Enhancers	Fetal Brain Female	brain
21	chr6:128813200-128814200	Enhancers	Fetal Stomach	stomach
22	chr6:128813200-128814200	Enhancers	Pancreas	Pancrea
23	chr6:128813200-128814200	Flanking Active TSS	A549	lung
24	chr6:128813200-128815000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr6:128813200-128815200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr6:128813200-128819200	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr6:128813200-128820400	Weak transcription	Fetal Kidney	kidney
28	chr6:128813400-128814000	Weak transcription	Right Ventricle	heart
29	chr6:128813400-128814000	Enhancers	NHDF-Ad	bronchial
30	chr6:128813400-128814200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr6:128813400-128814200	Enhancers	Liver	Liver
32	chr6:128813400-128814200	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr6:128813400-128814200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr6:128813400-128814200	Enhancers	Right Atrium	heart
35	chr6:128813400-128814200	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr6:128813400-128814200	Enhancers	HUVEC	blood vessel
37	chr6:128813400-128814800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr6:128813400-128814800	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr6:128813400-128814800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr6:128813400-128815000	Enhancers	NHLF	lung
41	chr6:128813400-128815400	Enhancers	Brain Substantia Nigra	brain
42	chr6:128813400-128815800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr6:128813400-128816800	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr6:128813400-128816800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr6:128813400-128816800	Weak transcription	Left Ventricle	heart
46	chr6:128813400-128817600	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr6:128813400-128819200	Weak transcription	Colonic Mucosa	Colon
48	chr6:128813400-128819200	Weak transcription	Fetal Brain Male	brain
49	chr6:128813400-128819400	Weak transcription	Psoas Muscle	Psoas
50	chr6:128813400-128820000	Enhancers	Fetal Intestine Small	intestine

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