Variant report

Variant	rs1643461
Chromosome Location	chr19:38468341-38468342
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	chr19:38463904..38465863-chr19:38467439..38469281,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10404159	0.88[EUR][1000 genomes]
rs10404567	0.88[CEU][hapmap];0.82[GIH][hapmap];0.82[TSI][hapmap]
rs10415399	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10415548	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs10420746	0.88[CEU][hapmap]
rs11083441	0.86[EUR][1000 genomes]
rs1119229	1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap]
rs12608883	0.88[EUR][1000 genomes]
rs12973580	0.85[EUR][1000 genomes]
rs1643460	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1643466	0.87[CEU][hapmap]
rs1643467	0.87[CEU][hapmap]
rs1643468	0.87[CEU][hapmap]
rs1725481	0.88[CEU][hapmap]
rs1725482	0.88[CEU][hapmap];0.82[GIH][hapmap]
rs1725499	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs2075281	0.88[CEU][hapmap]
rs28460297	0.88[EUR][1000 genomes]
rs353410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs353411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs353414	0.87[CEU][hapmap]
rs353415	0.88[CEU][hapmap]
rs353423	0.87[CEU][hapmap]
rs3786869	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes]
rs4239516	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes]
rs4802144	0.88[EUR][1000 genomes]
rs4802147	0.88[EUR][1000 genomes]
rs4803524	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs4803551	1.00[CEU][hapmap];0.90[CHB][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs4803573	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs705491	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs705492	0.88[CEU][hapmap]
rs705493	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs705494	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs705495	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs705499	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7250409	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs8102579	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs8108434	0.88[EUR][1000 genomes]
rs8109053	0.88[EUR][1000 genomes]
rs8109835	0.86[EUR][1000 genomes]
rs8110284	0.87[CEU][hapmap]
rs8113273	0.88[EUR][1000 genomes]
rs8113521	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs833895	0.87[CEU][hapmap]
rs833926	0.88[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1643461	PHLDB3	cis	cerebellum	SCAN
rs1643461	PAFAH1B3	cis	cerebellum	SCAN
rs1643461	CBLC	cis	parietal	SCAN
rs1643461	DMPK	cis	parietal	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38457200-38470400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:38457600-38470200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr19:38457600-38470400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr19:38457600-38470400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr19:38457800-38468400	Weak transcription	NH-A	brain
6	chr19:38458200-38468600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr19:38461600-38468400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr19:38461600-38468400	Weak transcription	Osteobl	bone
9	chr19:38461600-38468600	Weak transcription	Pancreas	Pancrea
10	chr19:38461600-38470200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr19:38461600-38470200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr19:38461600-38470200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr19:38461600-38470200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr19:38461600-38470400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr19:38461600-38470400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr19:38461600-38470400	Weak transcription	Gastric	stomach
17	chr19:38461600-38472000	Weak transcription	NHDF-Ad	bronchial
18	chr19:38461600-38476600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr19:38461600-38493600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr19:38461600-38493600	Weak transcription	Stomach Smooth Muscle	stomach
21	chr19:38461800-38470600	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr19:38461800-38476800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr19:38462000-38470200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr19:38462200-38470800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr19:38462200-38471800	Enhancers	Primary B cells from peripheral blood	blood
26	chr19:38463200-38468800	Weak transcription	Esophagus	oesophagus
27	chr19:38463400-38470400	Weak transcription	Colonic Mucosa	Colon
28	chr19:38463600-38469000	Weak transcription	Fetal Intestine Large	intestine
29	chr19:38463600-38476000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr19:38463800-38476200	Weak transcription	Primary hematopoietic stem cells	blood
31	chr19:38463800-38484800	Weak transcription	Fetal Stomach	stomach
32	chr19:38464000-38468400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr19:38464000-38470400	Weak transcription	Fetal Muscle Leg	muscle
34	chr19:38464200-38469800	Strong transcription	Fetal Intestine Small	intestine
35	chr19:38465200-38470200	Weak transcription	Liver	Liver
36	chr19:38465600-38468400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr19:38466000-38470200	Weak transcription	Stomach Mucosa	stomach
38	chr19:38466000-38472400	Weak transcription	Primary T cells from cord blood	blood
39	chr19:38466000-38475800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr19:38466200-38468400	Weak transcription	HSMM	muscle
41	chr19:38466200-38469600	Weak transcription	HepG2	liver
42	chr19:38466400-38468600	Enhancers	GM12878-XiMat	blood
43	chr19:38467400-38468600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr19:38467800-38471800	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr19:38468000-38469200	Enhancers	Brain Angular Gyrus	brain
46	chr19:38468000-38472000	Enhancers	Primary B cells from cord blood	blood
47	chr19:38468200-38468400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr19:38468200-38468400	Enhancers	Right Atrium	heart
49	chr19:38468200-38468600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr19:38468200-38468800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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