Variant report

Variant	rs17086769
Chromosome Location	chr4:57317578-57317579
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:57301296..57303911-chr4:57316208..57319458,3	MCF-7	breast:
2	chr4:57309697..57312077-chr4:57315535..57318192,2	MCF-7	breast:
3	chr4:57301960..57303479-chr4:57316742..57319608,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128059	Chromatin interaction
ENSG00000128050	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1401908	0.92[JPT][hapmap]
rs17086746	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17086755	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17086776	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17086786	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17086844	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17086879	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17086893	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17086906	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17086908	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17086924	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2292984	0.92[JPT][hapmap];0.92[EUR][1000 genomes]
rs28649329	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34228795	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34543011	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3796543	0.81[CHB][hapmap];0.92[JPT][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4074775	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41476944	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57439970	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58337902	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61580407	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61732641	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73155895	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73155901	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73157733	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73157739	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73157754	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73157769	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73157772	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73157774	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73157784	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73159992	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73162272	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73167378	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73167396	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7437329	0.93[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17086769	ARL9	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57303400-57330800	Weak transcription	Spleen	Spleen
2	chr4:57303800-57326000	Weak transcription	Gastric	stomach
3	chr4:57303800-57331000	Weak transcription	Stomach Mucosa	stomach
4	chr4:57303800-57332000	Weak transcription	Small Intestine	intestine
5	chr4:57304000-57330000	Weak transcription	Pancreas	Pancrea
6	chr4:57304000-57330000	Weak transcription	Right Ventricle	heart
7	chr4:57304000-57331800	Weak transcription	Esophagus	oesophagus
8	chr4:57304200-57318800	Weak transcription	Colon Smooth Muscle	Colon
9	chr4:57304200-57319200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr4:57304200-57331800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr4:57304400-57317800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr4:57304400-57318400	Weak transcription	Psoas Muscle	Psoas
13	chr4:57304400-57318600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr4:57304400-57319800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr4:57304400-57320200	Weak transcription	Fetal Heart	heart
16	chr4:57304400-57320200	Weak transcription	Rectal Smooth Muscle	rectum
17	chr4:57304400-57321200	Weak transcription	HSMMtube	muscle
18	chr4:57304400-57330800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr4:57304400-57330800	Weak transcription	Brain Substantia Nigra	brain
20	chr4:57304400-57331400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr4:57305800-57330400	Strong transcription	Fetal Thymus	thymus
22	chr4:57306200-57330200	Weak transcription	Brain Angular Gyrus	brain
23	chr4:57306200-57332200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr4:57306600-57323200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr4:57306600-57329400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr4:57306600-57330200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr4:57306600-57330400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:57306800-57321800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:57306800-57322200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr4:57306800-57330200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr4:57306800-57331000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr4:57307000-57325800	Strong transcription	HMEC	breast
33	chr4:57307000-57326200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr4:57307000-57330000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr4:57307200-57329600	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr4:57307400-57329000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr4:57307400-57329400	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr4:57307400-57329400	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr4:57307400-57329400	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr4:57307400-57329600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr4:57307400-57329800	Strong transcription	K562	blood
42	chr4:57307400-57330800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr4:57308000-57325800	Weak transcription	Colonic Mucosa	Colon
44	chr4:57308200-57328800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr4:57308400-57329000	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr4:57308800-57318800	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr4:57308800-57330000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr4:57309000-57330600	Weak transcription	Fetal Brain Male	brain
49	chr4:57309200-57321000	Weak transcription	Brain Anterior Caudate	brain
50	chr4:57310000-57319800	Weak transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links