Variant report

Variant	rs11570579
Chromosome Location	chr17:45197296-45197297
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs11079757	0.85[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11570481	0.95[ASN][1000 genomes]
rs11570495	0.95[ASN][1000 genomes]
rs11570513	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11570548	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11570565	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16941626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16941628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16941635	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1986817	0.85[ASN][1000 genomes]
rs34811916	0.86[ASN][1000 genomes]
rs55887846	0.81[ASN][1000 genomes]
rs717162	0.88[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72823425	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833466	chr17:45020360-45204537	Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	nsv833467	chr17:45063935-45252624	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv3332795	chr17:45116212-45209297	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	esv3386521	chr17:45116232-45209267	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv1059766	chr17:45130765-45203468	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	esv2760450	chr17:45130777-45225222	Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv908563	chr17:45158537-45230311	ZNF genes & repeats Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv962456	chr17:45163689-45212872	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers 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 target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11570579	IGFBP4	cis	parietal	SCAN
rs11570579	KRTAP4-1	cis	parietal	SCAN
rs11570579	MYL4	cis	Esophagus Muscularis	GTEx
rs11570579	PSMC3IP	cis	cerebellum	SCAN
rs11570579	MYL4	cis	lung	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45183400-45197400	Weak transcription	HSMMtube	muscle
2	chr17:45185600-45206400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr17:45186800-45197800	Weak transcription	Fetal Brain Female	brain
4	chr17:45188200-45197800	Weak transcription	Hela-S3	cervix
5	chr17:45189800-45198000	Weak transcription	Fetal Stomach	stomach
6	chr17:45190000-45203200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr17:45191000-45202000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr17:45191200-45197800	Weak transcription	Small Intestine	intestine
9	chr17:45191200-45202600	Weak transcription	Right Ventricle	heart
10	chr17:45191600-45197600	Weak transcription	HepG2	liver
11	chr17:45191800-45197600	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr17:45191800-45198000	Weak transcription	Thymus	Thymus
13	chr17:45192000-45198200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr17:45192200-45198000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr17:45192200-45198000	Weak transcription	Left Ventricle	heart
16	chr17:45192400-45197400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr17:45192400-45197600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr17:45192400-45212800	Weak transcription	Gastric	stomach
19	chr17:45192600-45197400	Weak transcription	Psoas Muscle	Psoas
20	chr17:45192600-45197600	Weak transcription	Fetal Kidney	kidney
21	chr17:45192600-45200200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr17:45192800-45197400	Weak transcription	HMEC	breast
23	chr17:45192800-45197600	Weak transcription	Primary T cells from cord blood	blood
24	chr17:45193200-45197800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr17:45193200-45212800	Weak transcription	Aorta	Aorta
26	chr17:45193400-45197400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr17:45193400-45197600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr17:45193600-45197400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr17:45193800-45197400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr17:45194000-45209800	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr17:45194200-45197400	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr17:45194200-45204600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr17:45194200-45208200	Strong transcription	HUVEC	blood vessel
34	chr17:45194200-45209600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr17:45194200-45209600	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr17:45194200-45209800	Strong transcription	Dnd41	blood
37	chr17:45194400-45197400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
38	chr17:45194400-45197400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr17:45194400-45197400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr17:45194400-45201000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr17:45194800-45197400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr17:45194800-45197400	Weak transcription	Brain Germinal Matrix	brain
43	chr17:45194800-45197600	Weak transcription	Brain Angular Gyrus	brain
44	chr17:45194800-45197600	Weak transcription	Brain Anterior Caudate	brain
45	chr17:45194800-45198000	Weak transcription	Fetal Muscle Leg	muscle
46	chr17:45194800-45198800	Weak transcription	Fetal Intestine Small	intestine
47	chr17:45194800-45203600	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr17:45194800-45212800	Weak transcription	Colonic Mucosa	Colon
49	chr17:45194800-45214400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr17:45194800-45234200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links