Variant report

Variant	rs4641803
Chromosome Location	chr17:16936194-16936195
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:16913150..16913949-chr17:16935742..16936397,2	MCF-7	breast:
2	chr17:16931293..16933179-chr17:16934223..16937186,2	MCF-7	breast:
3	chr17:16931573..16934044-chr17:16934220..16938314,3	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1047799	0.92[CHD][hapmap]
rs10852844	0.83[ASN][1000 genomes]
rs11078366	0.83[MEX][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs11078368	0.84[ASN][1000 genomes]
rs11078371	0.83[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11078372	0.83[ASN][1000 genomes]
rs11078373	0.83[CHB][hapmap];0.92[CHD][hapmap]
rs11651938	0.83[CHB][hapmap]
rs11652678	0.87[CHB][hapmap]
rs11654887	0.83[CHB][hapmap]
rs11657189	0.83[CHB][hapmap]
rs11870422	0.92[ASN][1000 genomes]
rs11870483	0.80[ASN][1000 genomes]
rs11870997	0.92[ASN][1000 genomes]
rs12451343	0.83[ASN][1000 genomes]
rs12601422	0.94[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.92[MKK][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12602592	0.83[CHB][hapmap]
rs12602839	0.84[ASN][1000 genomes]
rs12603417	0.84[ASN][1000 genomes]
rs1567815	0.83[CHB][hapmap]
rs1877631	0.83[MEX][hapmap];0.80[TSI][hapmap]
rs2292526	0.83[CHB][hapmap]
rs2292530	0.92[CHD][hapmap]
rs2349648	0.80[ASN][1000 genomes]
rs28452405	0.82[ASN][1000 genomes]
rs34001712	0.82[ASN][1000 genomes]
rs35650871	0.85[ASN][1000 genomes]
rs3744125	0.83[CHB][hapmap]
rs3744132	0.83[CHB][hapmap];0.92[CHD][hapmap]
rs3744134	0.90[CHD][hapmap]
rs3744136	0.83[CHB][hapmap]
rs3744137	0.92[CHD][hapmap]
rs3744138	0.92[CHD][hapmap]
rs3744139	0.92[CHD][hapmap]
rs4073688	0.90[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.81[ASN][1000 genomes]
rs4073940	0.88[MEX][hapmap]
rs4074612	0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4468683	0.81[ASN][1000 genomes]
rs4589617	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4629023	0.83[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.84[ASN][1000 genomes]
rs4985703	0.83[CHB][hapmap]
rs4985704	0.92[CHD][hapmap]
rs4985712	0.80[EUR][1000 genomes]
rs4985716	0.87[ASN][1000 genomes]
rs4985721	0.82[ASN][1000 genomes]
rs4985728	0.84[ASN][1000 genomes]
rs4985730	0.80[ASN][1000 genomes]
rs4985737	0.83[CHB][hapmap]
rs4985741	0.92[CHD][hapmap]
rs4985742	0.83[CHB][hapmap];0.92[CHD][hapmap];0.83[MEX][hapmap]
rs57729820	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs60128647	0.84[ASN][1000 genomes]
rs61242604	0.88[ASN][1000 genomes]
rs7212275	0.87[ASN][1000 genomes]
rs7214429	0.92[CHD][hapmap]
rs7218781	0.83[CHB][hapmap];0.92[CHD][hapmap]
rs73979060	0.84[ASN][1000 genomes]
rs73979078	0.84[ASN][1000 genomes]
rs8066234	0.92[CHD][hapmap]
rs8071254	0.88[ASN][1000 genomes]
rs8075751	0.83[CEU][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs8076273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9892695	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9906028	0.85[ASN][1000 genomes]
rs9907109	0.80[ASN][1000 genomes]
rs9910011	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058863	chr17:16812121-16943780	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv543227	chr17:16812121-16943780	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv907727	chr17:16892265-16938582	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv543231	chr17:16926227-16950644	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv978376	chr17:16934418-16938973	Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4641803	PAIP1	cis	parietal	SCAN
rs4641803	TOM1L2	cis	cerebellum	SCAN
rs4641803	MPRIP	cis	lymphoblastoid	seeQTL
rs4641803	M-RIP	Cis_1M	lymphoblastoid	RTeQTL
rs4641803	SMCR5	cis	parietal	SCAN
rs4641803	ALDH3A2	cis	parietal	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16930200-16936200	Enhancers	Fetal Muscle Leg	muscle
2	chr17:16930400-16936600	Enhancers	Fetal Muscle Trunk	muscle
3	chr17:16930600-16936200	Enhancers	HMEC	breast
4	chr17:16930600-16937600	Enhancers	HSMMtube	muscle
5	chr17:16931600-16936400	Enhancers	Fetal Lung	lung
6	chr17:16932200-16939800	Enhancers	Muscle Satellite Cultured Cells	--
7	chr17:16932400-16940600	Enhancers	HSMM	muscle
8	chr17:16932800-16944200	Weak transcription	Fetal Brain Female	brain
9	chr17:16933200-16936400	Enhancers	Brain Hippocampus Middle	brain
10	chr17:16933200-16936600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr17:16933200-16936800	Weak transcription	Fetal Thymus	thymus
12	chr17:16933400-16936200	Enhancers	Brain Cingulate Gyrus	brain
13	chr17:16933400-16936200	Enhancers	HUVEC	blood vessel
14	chr17:16933600-16936200	Enhancers	Hela-S3	cervix
15	chr17:16933600-16936200	Enhancers	NH-A	brain
16	chr17:16933800-16936200	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr17:16933800-16936200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr17:16933800-16936200	Enhancers	Fetal Heart	heart
19	chr17:16933800-16936800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr17:16934000-16936400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr17:16934200-16936200	Enhancers	Fetal Stomach	stomach
22	chr17:16934200-16936400	Enhancers	Osteobl	bone
23	chr17:16934200-16937800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr17:16934400-16936400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr17:16934400-16937400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr17:16934600-16936200	Enhancers	NHDF-Ad	bronchial
27	chr17:16934600-16936800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr17:16934600-16944600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr17:16934800-16936200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr17:16934800-16936200	Enhancers	Brain Substantia Nigra	brain
31	chr17:16935000-16936200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr17:16935000-16936200	Enhancers	Stomach Mucosa	stomach
33	chr17:16935000-16936600	Enhancers	Right Ventricle	heart
34	chr17:16935200-16936200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr17:16935200-16936200	Enhancers	Adipose Nuclei	Adipose
36	chr17:16935200-16936200	Enhancers	Liver	Liver
37	chr17:16935200-16936200	Enhancers	Brain Anterior Caudate	brain
38	chr17:16935200-16936200	Enhancers	Colon Smooth Muscle	Colon
39	chr17:16935200-16936200	Flanking Active TSS	HepG2	liver
40	chr17:16935200-16936400	Enhancers	K562	blood
41	chr17:16935200-16940800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr17:16935400-16936200	Enhancers	Fetal Intestine Small	intestine
43	chr17:16935400-16941200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr17:16935600-16937800	Weak transcription	Fetal Kidney	kidney
45	chr17:16935600-16944400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr17:16935800-16936200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
47	chr17:16935800-16936800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr17:16935800-16945200	Weak transcription	Aorta	Aorta
49	chr17:16936000-16937000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr17:16936000-16937000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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