Variant report

Variant	rs17364880
Chromosome Location	chr1:153889042-153889043
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:153888094..153890584-chr1:153918644..153920199,2	MCF-7	breast:
2	chr1:153887617..153890814-chr1:153892731..153897944,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143614	Chromatin interaction
ENSG00000198837	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10127484	1.00[JPT][hapmap]
rs10908578	1.00[JPT][hapmap]
rs11264573	1.00[JPT][hapmap]
rs11264736	1.00[JPT][hapmap]
rs11264972	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap]
rs12117078	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12142733	1.00[JPT][hapmap]
rs2230324	1.00[AFR][1000 genomes]
rs2252508	1.00[JPT][hapmap]
rs55874907	1.00[AFR][1000 genomes]
rs61804835	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6661009	1.00[JPT][hapmap]
rs7414227	1.00[JPT][hapmap]
rs7522030	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers 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	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS 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	136 gene(s)	inside rSNPs	diseases
4	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
5	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
6	nsv872450	chr1:153889042-153937513	Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS Weak 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 miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs17364880	TMOD4	cis	parietal	SCAN
rs17364880	KCTD14	trans	lymphoblastoid	seeQTL
rs17364880	PSMD4	cis	parietal	SCAN
rs17364880	INTS3	cis	lymphoblastoid	seeQTL
rs17364880	PGLYRP4	cis	cerebellum	SCAN
rs17364880	PI4KB	cis	cerebellum	SCAN
rs17364880	SLC27A3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153837000-153893000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:153846200-153894200	Weak transcription	Esophagus	oesophagus
3	chr1:153853800-153892200	Weak transcription	Pancreas	Pancrea
4	chr1:153853800-153893400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:153854000-153892600	Weak transcription	Colonic Mucosa	Colon
6	chr1:153854400-153892400	Weak transcription	Aorta	Aorta
7	chr1:153854600-153892200	Weak transcription	HSMM	muscle
8	chr1:153855000-153891800	Weak transcription	NHEK	skin
9	chr1:153855000-153892400	Weak transcription	NHLF	lung
10	chr1:153855000-153892800	Weak transcription	NH-A	brain
11	chr1:153855400-153892000	Weak transcription	HMEC	breast
12	chr1:153855600-153892200	Weak transcription	Fetal Kidney	kidney
13	chr1:153856000-153890400	Weak transcription	Brain Angular Gyrus	brain
14	chr1:153856000-153891600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:153860000-153890400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:153861200-153891600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr1:153861200-153892400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr1:153861400-153890800	Weak transcription	Colon Smooth Muscle	Colon
19	chr1:153862600-153892000	Weak transcription	Small Intestine	intestine
20	chr1:153866400-153894000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:153866600-153891600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:153866800-153892200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:153866800-153892200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr1:153870000-153892400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr1:153870200-153890400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr1:153870800-153892400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr1:153871800-153890600	Weak transcription	Brain Germinal Matrix	brain
28	chr1:153872000-153890800	Weak transcription	Fetal Brain Male	brain
29	chr1:153872000-153892400	Weak transcription	Placenta	Placenta
30	chr1:153872000-153892400	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr1:153872200-153890200	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr1:153872200-153892200	Weak transcription	Duodenum Mucosa	Duodenum
33	chr1:153872200-153892400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr1:153872400-153891800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:153872400-153891800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr1:153872800-153890200	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr1:153873200-153890200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:153873800-153890400	Weak transcription	Brain Anterior Caudate	brain
39	chr1:153874000-153891800	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr1:153874000-153892200	Weak transcription	Brain Substantia Nigra	brain
41	chr1:153874600-153892400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:153875400-153891600	Weak transcription	Right Atrium	heart
43	chr1:153876600-153890400	Weak transcription	Brain Cingulate Gyrus	brain
44	chr1:153876600-153890400	Weak transcription	Fetal Intestine Large	intestine
45	chr1:153876600-153892400	Weak transcription	Spleen	Spleen
46	chr1:153877200-153890400	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr1:153877400-153892200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:153877800-153892400	Weak transcription	NHDF-Ad	bronchial
49	chr1:153878000-153892400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:153878200-153891600	Weak transcription	Brain Hippocampus Middle	brain

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