Variant report

Variant	rs17305193
Chromosome Location	chr19:38089665-38089666
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	chr19:38085211..38087419-chr19:38088303..38090305,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000180479	Chromatin interaction
ENSG00000171817	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10445548	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1048505	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1061753	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061756	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12151156	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17244713	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17244769	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17303902	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17304703	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17305228	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17305823	0.96[CEU][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17306900	0.92[CEU][hapmap];0.86[ASN][1000 genomes]
rs1871196	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291001	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306201	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2385005	0.96[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35153242	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55681348	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55718806	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55743020	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55754546	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55865869	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55909413	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56277404	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56351266	0.86[ASN][1000 genomes]
rs57654288	0.98[EUR][1000 genomes]
rs57943942	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62108291	0.83[EUR][1000 genomes]
rs62108306	0.81[EUR][1000 genomes]
rs7245855	0.92[CEU][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7259272	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs73031330	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73033122	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73033134	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73033142	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73035159	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73035160	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73039029	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73041006	0.86[ASN][1000 genomes]
rs8101610	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104282	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104994	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8108268	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8111790	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs17305193	AC012309.5	cis	Esophagus Muscularis	GTEx
rs17305193	AC012309.5	cis	Artery Tibial	GTEx
rs17305193	AC012309.5	cis	Muscle Skeletal	GTEx
rs17305193	AC012309.5	cis	Thyroid	GTEx
rs17305193	ZNF781	cis	Thyroid	GTEx
rs17305193	AC012309.5	cis	Esophagus Mucosa	GTEx
rs17305193	AC012309.5	cis	lung	GTEx
rs17305193	AC012309.5	cis	Heart Left Ventricle	GTEx
rs17305193	AC012309.5	cis	Skin Sun Exposed Lower leg	GTEx
rs17305193	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38086400-38093400	Weak transcription	Gastric	stomach
2	chr19:38086400-38095600	Weak transcription	Fetal Muscle Trunk	muscle
3	chr19:38086400-38095600	Weak transcription	Stomach Mucosa	stomach
4	chr19:38086600-38089800	Weak transcription	Osteobl	bone
5	chr19:38086600-38090400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr19:38086600-38090800	Weak transcription	Psoas Muscle	Psoas
7	chr19:38086600-38091800	Weak transcription	Esophagus	oesophagus
8	chr19:38086600-38092000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr19:38086600-38092200	Weak transcription	Small Intestine	intestine
10	chr19:38086600-38092800	Weak transcription	Fetal Muscle Leg	muscle
11	chr19:38086600-38098200	Weak transcription	Colonic Mucosa	Colon
12	chr19:38086600-38098800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr19:38086600-38099400	Weak transcription	Fetal Stomach	stomach
14	chr19:38086600-38103200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr19:38086800-38090400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr19:38086800-38090400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr19:38086800-38090600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr19:38086800-38090800	Weak transcription	Fetal Intestine Large	intestine
19	chr19:38086800-38091800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr19:38086800-38092000	Weak transcription	Fetal Lung	lung
21	chr19:38086800-38094000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr19:38086800-38095600	Weak transcription	Fetal Kidney	kidney
23	chr19:38087200-38090400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr19:38087200-38090600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr19:38087200-38091800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr19:38087200-38093200	Weak transcription	Fetal Intestine Small	intestine
27	chr19:38087200-38099400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr19:38087200-38100200	Weak transcription	Right Ventricle	heart
29	chr19:38087200-38103000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr19:38087400-38090400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr19:38087400-38090400	Weak transcription	Dnd41	blood
32	chr19:38087400-38092000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr19:38087600-38091000	Weak transcription	Brain Germinal Matrix	brain
34	chr19:38087800-38094400	Weak transcription	Fetal Brain Male	brain
35	chr19:38087800-38107400	ZNF genes & repeats	Liver	Liver
36	chr19:38088000-38090800	Weak transcription	Fetal Brain Female	brain
37	chr19:38088800-38090600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr19:38088800-38090600	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr19:38088800-38092200	Strong transcription	Primary B cells from peripheral blood	blood
40	chr19:38088800-38093800	ZNF genes & repeats	Ovary	ovary
41	chr19:38088800-38094000	Strong transcription	Primary T cells from cord blood	blood
42	chr19:38088800-38094000	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr19:38088800-38094600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr19:38089000-38089800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr19:38089000-38090400	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr19:38089000-38090600	Weak transcription	Primary B cells from cord blood	blood
47	chr19:38089000-38090800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr19:38089000-38093400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
49	chr19:38089000-38093800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr19:38089000-38094000	Strong transcription	Skeletal Muscle Female	skeletal muscle

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