Variant report

Variant	rs2242595
Chromosome Location	chr17:18059454-18059455
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr17:18059437-18059456	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr17:18059454-18059477	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:18059406..18063498-chr17:18086302..18089651,4	K562	blood:
2	chr17:18041836..18044896-chr17:18058231..18061380,3	K562	blood:
3	chr17:18044305..18045021-chr17:18059355..18060391,3	MCF-7	breast:
4	chr17:18057503..18062681-chr17:18084968..18089396,8	MCF-7	breast:
5	chr17:18054836..18057146-chr17:18057563..18061410,3	MCF-7	breast:
6	chr17:18044150..18045078-chr17:18059256..18060265,3	MCF-7	breast:
7	chr17:18049467..18051833-chr17:18057367..18059688,2	MCF-7	breast:
8	chr17:18057350..18061680-chr17:18083813..18088656,8	K562	blood:
9	chr17:18055989..18058847-chr17:18059352..18061809,2	K562	blood:
10	chr17:18056639..18059705-chr17:18061625..18064659,3	MCF-7	breast:
11	chr17:18058869..18061487-chr17:18085234..18087160,2	MCF-7	breast:
12	chr17:18043317..18043875-chr17:18059389..18059944,2	MCF-7	breast:

No data

Variant related genes	Relation type
MYO15A	TF binding region
ENSG00000091536	Chromatin interaction
ENSG00000238691	Chromatin interaction
ENSG00000266677	Chromatin interaction
ENSG00000091542	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1064629	0.86[EUR][1000 genomes]
rs12449609	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12450483	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2056841	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2072652	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2072653	1.00[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2075659	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2124370	0.86[CEU][hapmap];0.82[GIH][hapmap]
rs2272571	1.00[ASW][hapmap];0.93[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4925145	0.80[CEU][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4925147	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57186648	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58804619	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59179192	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72827432	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8068517	0.93[CEU][hapmap];0.82[GIH][hapmap];0.93[MEX][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv482491	chr17:17959577-18153920	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1061162	chr17:17978838-18259234	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv492305	chr17:17980441-18424702	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
7	nsv907769	chr17:18000321-18064195	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv907770	chr17:18003845-18098018	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
9	nsv907771	chr17:18013560-18098018	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
10	nsv470580	chr17:18029857-18060192	Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
11	nsv907772	chr17:18030524-18098018	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
12	nsv510702	chr17:18037676-18116801	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2242595	SNORD49B	cis	cerebellum	SCAN
rs2242595	SHMT1	cis	multi-tissue	Pritchard

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18057200-18061400	Weak transcription	Primary T cells from cord blood	blood
2	chr17:18057400-18059600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr17:18057400-18060200	Weak transcription	HMEC	breast
4	chr17:18057400-18061000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr17:18057400-18061200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr17:18057400-18061200	Weak transcription	Small Intestine	intestine
7	chr17:18057400-18061400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr17:18057400-18061400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr17:18057600-18059800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr17:18057600-18060800	Weak transcription	Primary B cells from cord blood	blood
11	chr17:18057600-18060800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr17:18057600-18060800	Weak transcription	Placenta	Placenta
13	chr17:18057600-18061000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr17:18057600-18061000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr17:18057600-18061000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr17:18057600-18061000	Weak transcription	Lung	lung
17	chr17:18057600-18061000	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr17:18057600-18061200	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr17:18057600-18061200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr17:18057600-18061200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr17:18057600-18061200	Weak transcription	Esophagus	oesophagus
22	chr17:18057600-18061200	Weak transcription	Fetal Intestine Large	intestine
23	chr17:18057600-18061200	Weak transcription	Right Ventricle	heart
24	chr17:18057600-18061400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr17:18057600-18061400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr17:18057600-18061400	Weak transcription	Adipose Nuclei	Adipose
27	chr17:18057600-18061400	Weak transcription	Brain Angular Gyrus	brain
28	chr17:18057600-18061400	Weak transcription	Colonic Mucosa	Colon
29	chr17:18057600-18061400	Weak transcription	Fetal Intestine Small	intestine
30	chr17:18057600-18061400	Weak transcription	Left Ventricle	heart
31	chr17:18057600-18061400	Weak transcription	Pancreas	Pancrea
32	chr17:18057600-18061400	Weak transcription	Right Atrium	heart
33	chr17:18057600-18061400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr17:18057600-18061400	Weak transcription	HUVEC	blood vessel
35	chr17:18057600-18061400	Weak transcription	Osteobl	bone
36	chr17:18057600-18061600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr17:18057600-18061600	Weak transcription	Liver	Liver
38	chr17:18057600-18061600	Weak transcription	Brain Anterior Caudate	brain
39	chr17:18057600-18061600	Weak transcription	Psoas Muscle	Psoas
40	chr17:18057600-18061600	Weak transcription	NH-A	brain
41	chr17:18057600-18061800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr17:18057600-18061800	Weak transcription	NHDF-Ad	bronchial
43	chr17:18057600-18063000	Weak transcription	HSMMtube	muscle
44	chr17:18057800-18059600	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr17:18057800-18059800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr17:18057800-18059800	Weak transcription	K562	blood
47	chr17:18057800-18060000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr17:18057800-18060000	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr17:18057800-18060200	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr17:18057800-18060600	Weak transcription	HUES48 Cell Line	embryonic stem cell

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