Variant report

Variant	rs332857
Chromosome Location	chr19:38660797-38660798
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	chr19:38660797-38661158	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:38659478..38661172-chr19:38664692..38666456,2	K562	blood:
2	chr19:38660108..38661702-chr19:38665066..38666638,2	MCF-7	breast:
3	chr19:38655531..38657152-chr19:38659489..38661396,2	K562	blood:

Variant related genes	Relation type
SIPA1L3	TF binding region

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10460171	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11083447	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12460188	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12462587	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs12975576	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12984016	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12984380	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12984864	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12985707	0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1545039	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1962866	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2004981	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2010234	0.96[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2016074	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2116862	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2163817	0.89[EUR][1000 genomes]
rs2304132	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2382972	0.88[EUR][1000 genomes]
rs2382973	0.89[EUR][1000 genomes]
rs2569517	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs332841	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs332845	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs332846	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs332852	0.84[EUR][1000 genomes]
rs332854	0.90[EUR][1000 genomes]
rs332859	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs332860	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs332861	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs332862	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs332863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34646932	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35467693	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35469521	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35972455	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3852910	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3852911	0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4802248	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4803805	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4803808	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67910767	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71337549	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7253312	0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7253633	0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7258019	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8100956	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8107385	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs855617	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
2	nsv833821	chr19:38629937-38756792	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv911657	chr19:38655449-38753786	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38638200-38667200	Strong transcription	Cortex derived primary cultured neurospheres	brain
2	chr19:38645600-38660800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr19:38646000-38661000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr19:38653400-38661400	Strong transcription	Rectal Mucosa Donor 29	rectum
5	chr19:38653400-38663400	Strong transcription	Sigmoid Colon	Sigmoid Colon
6	chr19:38653600-38661200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr19:38653600-38661200	Strong transcription	Duodenum Mucosa	Duodenum
8	chr19:38653600-38661400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr19:38653600-38661400	Strong transcription	Rectal Mucosa Donor 31	rectum
10	chr19:38653600-38661600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr19:38653600-38663200	Strong transcription	Gastric	stomach
12	chr19:38653600-38663400	Weak transcription	HUVEC	blood vessel
13	chr19:38653600-38663800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr19:38653600-38663800	Strong transcription	Fetal Intestine Large	intestine
15	chr19:38653600-38665200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr19:38653600-38668600	Strong transcription	Primary B cells from peripheral blood	blood
17	chr19:38653600-38696400	Weak transcription	Small Intestine	intestine
18	chr19:38653800-38661600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr19:38653800-38661600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr19:38653800-38662400	Weak transcription	Brain Substantia Nigra	brain
21	chr19:38653800-38663600	Weak transcription	HMEC	breast
22	chr19:38653800-38663800	Strong transcription	Fetal Intestine Small	intestine
23	chr19:38653800-38664000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr19:38653800-38666600	Strong transcription	A549	lung
25	chr19:38653800-38670800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr19:38654000-38663000	Weak transcription	NHEK	skin
27	chr19:38654000-38664000	Strong transcription	Fetal Stomach	stomach
28	chr19:38654200-38661000	Strong transcription	Liver	Liver
29	chr19:38654200-38661600	Strong transcription	Osteobl	bone
30	chr19:38655000-38661600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr19:38655200-38669400	Weak transcription	Fetal Lung	lung
32	chr19:38656200-38660800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr19:38656200-38660800	Weak transcription	Brain Cingulate Gyrus	brain
34	chr19:38656200-38660800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr19:38656200-38661000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr19:38656200-38661000	Weak transcription	Aorta	Aorta
37	chr19:38656200-38662200	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr19:38656200-38662400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr19:38656200-38663400	Weak transcription	HSMM	muscle
40	chr19:38656200-38664200	Weak transcription	HSMMtube	muscle
41	chr19:38656200-38664200	Weak transcription	NHDF-Ad	bronchial
42	chr19:38656200-38675200	Weak transcription	Stomach Mucosa	stomach
43	chr19:38656400-38662400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr19:38656400-38663800	Weak transcription	Right Ventricle	heart
45	chr19:38656400-38670400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr19:38656400-38670400	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr19:38656400-38670800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr19:38656400-38671400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr19:38656400-38674000	Weak transcription	Colon Smooth Muscle	Colon
50	chr19:38656600-38661200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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