Variant report

Variant	rs13201757
Chromosome Location	chr6:31087060-31087061
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:31085584..31087243-chr6:31091042..31093736,2	K562	blood:
2	chr6:30708872..30711797-chr6:31085537..31087633,2	MCF-7	breast:
3	chr6:31081100..31082807-chr6:31085886..31088113,2	MCF-7	breast:
4	chr6:31079457..31085209-chr6:31085850..31092700,13	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204540	Chromatin interaction
ENSG00000137312	Chromatin interaction
ENSG00000272273	Chromatin interaction
ENSG00000204542	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12191286	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12195316	0.82[EUR][1000 genomes]
rs12197796	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12199460	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12201248	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12204500	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12214039	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13198298	0.80[EUR][1000 genomes]
rs13204986	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13212902	0.90[AMR][1000 genomes]
rs17196961	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28732092	0.82[EUR][1000 genomes]
rs3734852	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3778639	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3778640	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6909321	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6929464	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6931921	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6932086	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7756290	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv1029442	chr6:31006647-31449207	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
7	nsv427750	chr6:31028290-31234581	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv428140	chr6:31028290-31462106	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	89 gene(s)	inside rSNPs	diseases
9	esv2758042	chr6:31028290-31497106	Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	101 gene(s)	inside rSNPs	diseases
10	esv2759414	chr6:31028290-31542308	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	151 gene(s)	inside rSNPs	diseases
11	nsv1033227	chr6:31071547-31101674	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv525933	chr6:31081205-31142245	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
13	nsv462747	chr6:31082361-31092124	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv601491	chr6:31082361-31092124	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	nsv884137	chr6:31082361-31129310	Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
16	esv1797052	chr6:31083813-31095816	Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
17	esv1820685	chr6:31083813-31097453	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13201757	XXbac-BPG248L24.12	cis	Artery Tibial	GTEx
rs13201757	XXbac-BPG248L24.12	cis	Thyroid	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31082600-31092800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr6:31082800-31093000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:31083200-31092800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:31083200-31094200	Weak transcription	Aorta	Aorta
5	chr6:31083200-31105400	Weak transcription	Spleen	Spleen
6	chr6:31083400-31087800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:31083400-31090000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr6:31083400-31093400	Weak transcription	HSMMtube	muscle
9	chr6:31083600-31091000	Weak transcription	A549	lung
10	chr6:31083600-31092600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr6:31083800-31089600	Weak transcription	HUVEC	blood vessel
12	chr6:31083800-31090000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr6:31083800-31090200	Weak transcription	HSMM	muscle
14	chr6:31083800-31093600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr6:31084400-31089200	Weak transcription	Gastric	stomach
16	chr6:31085200-31090000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr6:31085400-31087200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr6:31085400-31088000	Weak transcription	HMEC	breast
19	chr6:31085400-31090000	Weak transcription	Colon Smooth Muscle	Colon
20	chr6:31085400-31090000	Weak transcription	Right Ventricle	heart
21	chr6:31085400-31090000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr6:31085400-31090200	Weak transcription	Esophagus	oesophagus
23	chr6:31085400-31090200	Weak transcription	Left Ventricle	heart
24	chr6:31085400-31090200	Weak transcription	Ovary	ovary
25	chr6:31085400-31090600	Weak transcription	Brain Substantia Nigra	brain
26	chr6:31085400-31090600	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr6:31085400-31090600	Weak transcription	Pancreas	Pancrea
28	chr6:31085400-31090600	Weak transcription	Stomach Mucosa	stomach
29	chr6:31085600-31090600	Weak transcription	Right Atrium	heart
30	chr6:31085600-31093200	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr6:31085800-31087200	Enhancers	Lung	lung
32	chr6:31086400-31088200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr6:31086400-31088200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:31086400-31089800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr6:31086600-31088000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr6:31086600-31088000	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr6:31086600-31088000	Weak transcription	NHEK	skin
38	chr6:31086800-31087200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links