Variant report

Variant	rs478582
Chromosome Location	chr18:12835976-12835977
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	chr18:12833814..12836436-chr18:12879380..12882256,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12957037	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12971201	1.00[ASW][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2542152	0.81[CEU][hapmap];0.84[MKK][hapmap];0.88[YRI][hapmap]
rs2542157	0.81[CEU][hapmap];0.93[GIH][hapmap];0.84[MKK][hapmap];0.88[YRI][hapmap]
rs2542160	0.90[GIH][hapmap]
rs2542162	1.00[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2847273	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2847281	1.00[ASW][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2847286	0.86[GIH][hapmap];0.88[YRI][hapmap]
rs2847298	0.87[YRI][hapmap]
rs2852151	0.92[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3826557	0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4797709	0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs559406	0.99[ASN][1000 genomes]
rs588447	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs592390	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs641085	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs674222	0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs8087237	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];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs888271	0.81[CEU][hapmap];0.88[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
3	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
5	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
6	nsv1064844	chr18:12748045-12953235	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
7	nsv543656	chr18:12748045-12953235	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs478582	FAM71E2	trans	parietal	SCAN
rs478582	RP11-973H7.4	cis	Whole Blood	GTEx
rs478582	FAM38B	cis	cerebellum	SCAN
rs478582	PTPN2	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12777800-12838200	Weak transcription	Colonic Mucosa	Colon
2	chr18:12791400-12837000	Weak transcription	NHDF-Ad	bronchial
3	chr18:12802000-12842400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr18:12807200-12842400	Weak transcription	Fetal Heart	heart
5	chr18:12809600-12838200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr18:12809600-12838200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr18:12812000-12838400	Weak transcription	Right Ventricle	heart
8	chr18:12814400-12843400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr18:12817800-12837600	Weak transcription	NH-A	brain
10	chr18:12820000-12836400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr18:12820400-12838600	Weak transcription	Brain Angular Gyrus	brain
12	chr18:12820800-12837600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr18:12820800-12838200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr18:12820800-12838200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr18:12821000-12840400	Weak transcription	Brain Substantia Nigra	brain
16	chr18:12821400-12836800	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr18:12821600-12839200	Weak transcription	Brain Anterior Caudate	brain
18	chr18:12821800-12851800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr18:12823000-12837600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr18:12823400-12836200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr18:12825400-12838200	Weak transcription	Gastric	stomach
22	chr18:12825400-12840400	Weak transcription	Spleen	Spleen
23	chr18:12825600-12838200	Weak transcription	Aorta	Aorta
24	chr18:12825600-12838200	Weak transcription	K562	blood
25	chr18:12826000-12838400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr18:12826400-12837800	Weak transcription	Fetal Brain Male	brain
27	chr18:12826800-12838200	Weak transcription	Pancreas	Pancrea
28	chr18:12827200-12836600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr18:12827600-12838200	Weak transcription	Esophagus	oesophagus
30	chr18:12827600-12838200	Weak transcription	Small Intestine	intestine
31	chr18:12827600-12838400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr18:12827600-12843400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr18:12827800-12836200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr18:12828400-12836600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr18:12828400-12836600	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr18:12828400-12837600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr18:12828400-12837600	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr18:12828400-12842600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr18:12828400-12856000	Weak transcription	Fetal Kidney	kidney
40	chr18:12828600-12836400	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr18:12828800-12836400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr18:12828800-12836600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr18:12828800-12837000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr18:12828800-12837200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr18:12828800-12837600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr18:12828800-12838200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr18:12828800-12838200	Weak transcription	Psoas Muscle	Psoas
48	chr18:12829000-12836200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr18:12829000-12836600	Weak transcription	A549	lung
50	chr18:12829000-12836600	Weak transcription	NHLF	lung

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