Variant report

Variant	rs17086755
Chromosome Location	chr4:57277416-57277417
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:57277188-57277564	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:57256866..57258507-chr4:57276793..57279015,2	K562	blood:
2	chr4:57274956..57277925-chr4:57332751..57335099,2	MCF-7	breast:
3	chr4:57275711..57277429-chr4:57298915..57301727,2	K562	blood:

Variant related genes	Relation type
PPAT	TF binding region
ENSG00000174780	Chromatin interaction
ENSG00000128059	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1401908	0.91[JPT][hapmap]
rs17086746	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17086769	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17086776	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17086786	0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17086844	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17086879	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17086893	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17086906	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17086908	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17086924	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2292984	0.83[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28649329	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34228795	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34543011	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3796543	0.92[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4074775	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41476944	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57439970	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58337902	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59161426	0.80[ASN][1000 genomes]
rs61580407	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61732641	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73155895	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73155901	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73157733	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73157739	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73157754	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73157769	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73157772	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73157774	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73157784	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73159992	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73162272	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73167378	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73167396	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7437329	0.92[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	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
5	nsv4347	chr4:57261404-57280595	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv1801975	chr4:57267406-57297335	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17086755	ARL9	cis	multi-tissue	Pritchard

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57254600-57280200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:57254800-57287600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:57264200-57290200	Weak transcription	Esophagus	oesophagus
4	chr4:57264800-57301000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:57265000-57301000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:57267800-57277600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr4:57267800-57278400	Weak transcription	Placenta	Placenta
8	chr4:57272600-57280200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr4:57272800-57280400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr4:57272800-57281600	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr4:57272800-57292600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr4:57272800-57299800	Weak transcription	Primary T cells from cord blood	blood
13	chr4:57272800-57299800	Weak transcription	Fetal Thymus	thymus
14	chr4:57272800-57300000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr4:57274000-57287000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr4:57274000-57290600	Weak transcription	GM12878-XiMat	blood
17	chr4:57274200-57287000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr4:57274200-57296400	Weak transcription	Dnd41	blood
19	chr4:57275000-57278200	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr4:57275000-57278400	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr4:57275200-57278000	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr4:57275400-57277800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr4:57275400-57278200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr4:57275400-57278200	Enhancers	NHDF-Ad	bronchial
25	chr4:57275600-57277600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr4:57276200-57278000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr4:57276200-57278000	Active TSS	Brain Anterior Caudate	brain
28	chr4:57276200-57280200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr4:57276400-57278000	Active TSS	Brain Inferior Temporal Lobe	brain
30	chr4:57276400-57278000	Enhancers	HepG2	liver
31	chr4:57276400-57278600	Active TSS	Brain Angular Gyrus	brain
32	chr4:57276600-57278200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr4:57276600-57278600	Enhancers	K562	blood
34	chr4:57276800-57277800	Enhancers	Hela-S3	cervix
35	chr4:57276800-57278200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr4:57276800-57284200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr4:57277000-57277800	Active TSS	Fetal Brain Female	brain
38	chr4:57277000-57277800	Enhancers	Rectal Smooth Muscle	rectum
39	chr4:57277000-57277800	Enhancers	A549	lung
40	chr4:57277000-57278000	Active TSS	Brain Cingulate Gyrus	brain
41	chr4:57277000-57278000	Enhancers	NHEK	skin
42	chr4:57277000-57278200	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr4:57277000-57278400	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr4:57277000-57278600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr4:57277000-57278800	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr4:57277000-57279400	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr4:57277000-57280200	Weak transcription	Colon Smooth Muscle	Colon
48	chr4:57277000-57280200	Weak transcription	Duodenum Mucosa	Duodenum
49	chr4:57277000-57280400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr4:57277000-57287200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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