Variant report

Variant	rs8066529
Chromosome Location	chr17:46187565-46187566
allele	C/T
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	chr17:46185296-46189875	K562	blood:	n/a	n/a
2	STAT3	chr17:46187564-46188083	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:46184602..46186632-chr17:46186895..46189927,3	MCF-7	breast:
2	chr17:46175023..46180196-chr17:46181333..46189268,23	MCF-7	breast:
3	chr17:46125014..46129511-chr17:46182877..46189561,8	K562	blood:
4	chr17:46179911..46181951-chr17:46186605..46188187,2	K562	blood:

Variant related genes	Relation type
SNX11	TF binding region
ENSG00000108468	Chromatin interaction
ENSG00000002919	Chromatin interaction
ENSG00000263412	Chromatin interaction
ENSG00000082641	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10853093	0.81[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs11079815	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11079817	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11655781	0.87[CHD][hapmap];0.85[LWK][hapmap]
rs11870317	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12452103	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1349676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1377201	1.00[CHB][hapmap]
rs1452661	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs188268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1910574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs208006	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs208007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs208013	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs208017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs208018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2123342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2325886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28439030	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28551638	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2924253	1.00[CHB][hapmap]
rs2924255	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2924256	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2924258	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2938471	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2938480	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2938482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2957932	1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[LWK][hapmap];0.82[ASN][1000 genomes]
rs2957933	1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[LWK][hapmap];0.82[ASN][1000 genomes]
rs3792693	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4794426	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4794427	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4794467	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4794488	0.81[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs5016303	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs595874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6504100	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6504101	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6504113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7207270	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7208796	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7213530	0.88[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7216766	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7220940	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7225140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8071262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8077814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8079982	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8081199	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8182234	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs979746	1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[LWK][hapmap];0.82[ASN][1000 genomes]
rs9893405	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9899753	1.00[JPT][hapmap]
rs9905460	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]

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	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS 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 miRNA target site	85 gene(s)	inside rSNPs	diseases
3	nsv908576	chr17:46147807-46260366	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
4	nsv112217	chr17:46182711-46190093	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8066529	AARSD1	cis	parietal	SCAN
rs8066529	HOXB2	cis	parietal	SCAN
rs8066529	MLX	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46185600-46191000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr17:46185800-46188200	Weak transcription	Left Ventricle	heart
3	chr17:46185800-46188200	Weak transcription	Pancreas	Pancrea
4	chr17:46185800-46190000	Weak transcription	Lung	lung
5	chr17:46185800-46193000	Weak transcription	Gastric	stomach
6	chr17:46185800-46195800	Weak transcription	Ovary	ovary
7	chr17:46186000-46188400	Enhancers	Brain Substantia Nigra	brain
8	chr17:46186000-46189200	Weak transcription	Colonic Mucosa	Colon
9	chr17:46186000-46195200	Weak transcription	Aorta	Aorta
10	chr17:46186000-46196200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr17:46186000-46198600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr17:46186200-46187600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr17:46186200-46187600	Weak transcription	Brain Anterior Caudate	brain
14	chr17:46186200-46187600	Weak transcription	Right Ventricle	heart
15	chr17:46186200-46187800	Enhancers	Primary B cells from peripheral blood	blood
16	chr17:46186200-46188200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr17:46186200-46188400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr17:46186200-46188600	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr17:46186200-46189000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr17:46186200-46189400	Weak transcription	Placenta	Placenta
21	chr17:46186200-46189600	Weak transcription	Fetal Muscle Leg	muscle
22	chr17:46186200-46189600	Weak transcription	Thymus	Thymus
23	chr17:46186200-46189800	Weak transcription	Fetal Stomach	stomach
24	chr17:46186200-46190000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr17:46186200-46190400	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr17:46186200-46190400	Weak transcription	Esophagus	oesophagus
27	chr17:46186200-46190400	Weak transcription	Fetal Kidney	kidney
28	chr17:46186200-46190600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr17:46186200-46190600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr17:46186200-46192000	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr17:46186200-46192600	Weak transcription	Colon Smooth Muscle	Colon
32	chr17:46186200-46192600	Weak transcription	A549	lung
33	chr17:46186200-46193800	Weak transcription	Fetal Lung	lung
34	chr17:46186200-46195000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr17:46186200-46195200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr17:46186200-46196200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr17:46186200-46198600	Weak transcription	Fetal Brain Male	brain
38	chr17:46186200-46203600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr17:46186400-46187600	Weak transcription	Brain Cingulate Gyrus	brain
40	chr17:46186400-46187600	Weak transcription	HepG2	liver
41	chr17:46186400-46187800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr17:46186400-46187800	Enhancers	K562	blood
43	chr17:46186400-46188000	Weak transcription	Liver	Liver
44	chr17:46186400-46188200	Weak transcription	Fetal Intestine Small	intestine
45	chr17:46186400-46188200	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr17:46186400-46188200	Weak transcription	HUVEC	blood vessel
47	chr17:46186400-46188400	Weak transcription	Primary T cells from cord blood	blood
48	chr17:46186400-46188400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr17:46186400-46188600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr17:46186400-46189200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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