Variant report

Variant	rs60547490
Chromosome Location	chr6:56763451-56763452
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11963379	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11965554	1.00[AMR][1000 genomes]
rs11969595	1.00[AMR][1000 genomes]
rs1599281	1.00[ASN][1000 genomes]
rs17450853	1.00[ASN][1000 genomes]
rs17685185	1.00[ASN][1000 genomes]
rs17752412	1.00[ASN][1000 genomes]
rs17752435	1.00[ASN][1000 genomes]
rs28432154	1.00[AMR][1000 genomes]
rs34752771	1.00[ASN][1000 genomes]
rs35527216	1.00[ASN][1000 genomes]
rs4490669	1.00[ASN][1000 genomes]
rs59524770	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60910643	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60962957	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61340009	1.00[ASN][1000 genomes]
rs73459728	0.91[ASN][1000 genomes]
rs73459729	1.00[ASN][1000 genomes]
rs73459735	1.00[ASN][1000 genomes]
rs73463711	1.00[ASN][1000 genomes]
rs748996	1.00[ASN][1000 genomes]
rs9464406	0.83[AMR][1000 genomes]
rs9464408	1.00[AMR][1000 genomes]
rs9475742	1.00[AMR][1000 genomes]
rs9475743	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9475745	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9475746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9475750	1.00[AMR][1000 genomes]
rs9475751	0.83[AMR][1000 genomes]
rs9475752	1.00[ASN][1000 genomes]
rs9475754	1.00[AMR][1000 genomes]
rs9475755	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv1022714	chr6:56729767-56826642	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv538229	chr6:56729767-56826642	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv508408	chr6:56735681-56773285	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv5315	chr6:56752042-56798761	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
10	esv1002581	chr6:56758291-56767820	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56749200-56769600	Weak transcription	Brain Angular Gyrus	brain
2	chr6:56752400-56767000	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr6:56753600-56769600	Weak transcription	Brain Hippocampus Middle	brain
4	chr6:56756000-56767000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr6:56756000-56767400	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr6:56756000-56769600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr6:56756000-56769600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr6:56756000-56770000	Weak transcription	Brain Substantia Nigra	brain
9	chr6:56756200-56764000	Weak transcription	NH-A	brain
10	chr6:56756200-56767200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:56756200-56768400	Weak transcription	HMEC	breast
12	chr6:56756200-56768600	Weak transcription	HUVEC	blood vessel
13	chr6:56756200-56768800	Weak transcription	NHEK	skin
14	chr6:56756600-56767000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr6:56756600-56775800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:56756800-56763800	Weak transcription	HSMMtube	muscle
17	chr6:56756800-56771600	Weak transcription	K562	blood
18	chr6:56757000-56763800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:56757200-56763600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr6:56757200-56767400	Weak transcription	GM12878-XiMat	blood
21	chr6:56759600-56767000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr6:56761000-56763600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr6:56761000-56764600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr6:56761000-56767400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr6:56761400-56763600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr6:56762200-56765000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr6:56762400-56763600	Strong transcription	Brain Cingulate Gyrus	brain
28	chr6:56762400-56763600	Strong transcription	NHDF-Ad	bronchial
29	chr6:56762400-56764400	Enhancers	Fetal Intestine Small	intestine
30	chr6:56762400-56765000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr6:56762400-56765600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:56762400-56766600	Weak transcription	Fetal Stomach	stomach
33	chr6:56762600-56763800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr6:56762600-56764000	Enhancers	Fetal Intestine Large	intestine
35	chr6:56762600-56764000	Enhancers	A549	lung
36	chr6:56762600-56765000	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr6:56762800-56763800	Weak transcription	NHLF	lung
38	chr6:56762800-56764200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr6:56762800-56764800	Weak transcription	Colonic Mucosa	Colon
40	chr6:56763000-56763600	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr6:56763000-56763600	Weak transcription	HSMM	muscle
42	chr6:56763000-56763800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr6:56763000-56764200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr6:56763000-56764200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr6:56763000-56765400	Enhancers	Rectal Smooth Muscle	rectum
46	chr6:56763200-56763600	Enhancers	HepG2	liver
47	chr6:56763400-56765000	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr6:56763400-56765200	Enhancers	Colon Smooth Muscle	Colon
49	chr6:56763400-56765200	Genic enhancers	Osteobl	bone
50	chr6:56763400-56765400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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