Variant report

Variant	rs10485163
Chromosome Location	chr6:128816888-128816889
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	FOXA2	chr6:128816812-128818204	HepG2	liver:	n/a	chr6:128817857-128817869
2	MBD4	chr6:128816784-128817424	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:128813517..128817980-chr6:128840263..128842508,4	MCF-7	breast:
2	chr6:128808264..128811474-chr6:128816521..128819599,3	K562	blood:

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

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs13196432	1.00[ASN][1000 genomes]
rs1417895	1.00[CHD][hapmap];1.00[MEX][hapmap]
rs17055770	1.00[ASW][hapmap]
rs17055897	1.00[CEU][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17055911	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17459522	1.00[CHD][hapmap];0.89[MKK][hapmap];1.00[ASN][1000 genomes]
rs1891149	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs1935129	1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs6569528	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6937769	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs9375570	1.00[CHD][hapmap]
rs9491952	1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs9491954	1.00[ASN][1000 genomes]
rs9491955	1.00[ASN][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:79 , 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	chr6:128812000-128817000	Genic enhancers	HepG2	liver
4	chr6:128812200-128817200	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr6:128812800-128819400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr6:128813000-128817800	Enhancers	Stomach Mucosa	stomach
7	chr6:128813000-128828600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:128813200-128819200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr6:128813200-128820400	Weak transcription	Fetal Kidney	kidney
10	chr6:128813400-128817600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr6:128813400-128819200	Weak transcription	Colonic Mucosa	Colon
12	chr6:128813400-128819200	Weak transcription	Fetal Brain Male	brain
13	chr6:128813400-128819400	Weak transcription	Psoas Muscle	Psoas
14	chr6:128813400-128820000	Enhancers	Fetal Intestine Small	intestine
15	chr6:128813400-128820000	Enhancers	Rectal Mucosa Donor 31	rectum
16	chr6:128813400-128825400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:128813600-128817800	Enhancers	Duodenum Mucosa	Duodenum
18	chr6:128813600-128819200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr6:128813600-128820400	Weak transcription	HSMM	muscle
20	chr6:128814000-128819200	Weak transcription	NH-A	brain
21	chr6:128814000-128825200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr6:128814200-128818600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr6:128814200-128819000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr6:128814200-128819200	Weak transcription	Colon Smooth Muscle	Colon
25	chr6:128814200-128819200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr6:128814200-128821200	Weak transcription	Osteobl	bone
27	chr6:128814200-128821800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:128814200-128822200	Weak transcription	Fetal Stomach	stomach
29	chr6:128814200-128824800	Weak transcription	Right Ventricle	heart
30	chr6:128814600-128817200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:128814600-128818000	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr6:128814800-128817400	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr6:128814800-128817400	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr6:128814800-128817600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr6:128814800-128819200	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr6:128815000-128817200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr6:128815000-128820400	Weak transcription	NHEK	skin
38	chr6:128815000-128821200	Weak transcription	NHLF	lung
39	chr6:128815200-128817200	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr6:128815200-128833800	Enhancers	Fetal Intestine Large	intestine
41	chr6:128815400-128819400	Weak transcription	Right Atrium	heart
42	chr6:128815600-128822600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:128815800-128817200	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr6:128815800-128819200	Weak transcription	Stomach Smooth Muscle	stomach
45	chr6:128815800-128819600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr6:128815800-128822800	Weak transcription	Fetal Thymus	thymus
47	chr6:128816000-128817200	Enhancers	Brain Hippocampus Middle	brain
48	chr6:128816000-128819200	Weak transcription	Fetal Lung	lung
49	chr6:128816000-128819200	Weak transcription	HSMMtube	muscle
50	chr6:128816000-128819400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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