Variant report

Variant	rs2232801
Chromosome Location	chr19:44676148-44676149
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:44675915..44677580-chr19:44681750..44683462,2	K562	blood:
2	chr19:44669226..44671840-chr19:44675561..44678449,3	K562	blood:

Variant related genes	Relation type
ENSG00000167380	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10405450	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10410086	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10423306	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10425945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11667521	0.85[CEU][hapmap];0.93[GIH][hapmap];0.86[TSI][hapmap]
rs12459795	0.90[EUR][1000 genomes]
rs12460039	0.97[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs12462557	0.85[CEU][hapmap];0.90[GIH][hapmap];0.86[TSI][hapmap]
rs12462723	0.85[CEU][hapmap];0.90[GIH][hapmap];0.86[TSI][hapmap]
rs12608984	0.91[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs12972784	0.86[EUR][1000 genomes]
rs12975546	0.85[CEU][hapmap]
rs12980565	0.85[CEU][hapmap]
rs2051059	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs2085516	0.91[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs2100643	0.91[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs2125579	0.85[CEU][hapmap];0.83[GIH][hapmap];0.86[TSI][hapmap]
rs2168989	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2279072	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2279073	0.85[CEU][hapmap];0.93[GIH][hapmap];0.86[TSI][hapmap]
rs2293587	0.87[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.91[ASN][1000 genomes]
rs2356751	0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.91[ASN][1000 genomes]
rs3817595	0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.91[ASN][1000 genomes]
rs4802218	0.84[CEU][hapmap]
rs56357907	0.95[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs58778698	0.91[ASN][1000 genomes]
rs60668498	0.85[ASN][1000 genomes]
rs61412562	0.87[ASN][1000 genomes]
rs61589395	0.87[ASN][1000 genomes]
rs62117770	0.95[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6509146	0.91[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs7248114	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7249209	0.91[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs7251682	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7253196	0.83[EUR][1000 genomes]
rs7253533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7259916	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7260304	1.00[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8101032	0.85[CEU][hapmap]
rs8102037	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8105073	0.87[CEU][hapmap]
rs8108934	0.87[EUR][1000 genomes]
rs9304640	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9646643	0.85[CEU][hapmap];0.92[GIH][hapmap];0.86[TSI][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	nsv833840	chr19:44520620-44715760	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2232801	SIGLEC16	cis	cerebellum	SCAN
rs2232801	SAE1	cis	cerebellum	SCAN
rs2232801	SIX5	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44670000-44677000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:44670400-44680200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr19:44670600-44678800	Strong transcription	Fetal Muscle Trunk	muscle
4	chr19:44670600-44679000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr19:44670600-44681600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
6	chr19:44670600-44688200	ZNF genes & repeats	Liver	Liver
7	chr19:44670800-44677000	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr19:44670800-44677000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr19:44670800-44677000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr19:44670800-44678000	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr19:44670800-44678000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr19:44670800-44678400	ZNF genes & repeats	Fetal Intestine Large	intestine
13	chr19:44670800-44678800	Strong transcription	Osteobl	bone
14	chr19:44670800-44679000	Strong transcription	Muscle Satellite Cultured Cells	--
15	chr19:44670800-44679400	Strong transcription	NH-A	brain
16	chr19:44670800-44679600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr19:44670800-44679800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr19:44670800-44680000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr19:44670800-44680200	Strong transcription	HSMMtube	muscle
20	chr19:44670800-44680400	Strong transcription	Fetal Thymus	thymus
21	chr19:44670800-44681200	ZNF genes & repeats	Ovary	ovary
22	chr19:44670800-44681800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr19:44670800-44682000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
24	chr19:44670800-44682000	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
25	chr19:44670800-44682200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr19:44670800-44683000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
27	chr19:44670800-44683200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
28	chr19:44671000-44678600	Strong transcription	HMEC	breast
29	chr19:44671000-44679000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr19:44671000-44679000	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr19:44671000-44679200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr19:44671000-44680400	Strong transcription	Placenta	Placenta
33	chr19:44671000-44681800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr19:44671200-44680600	Strong transcription	Placenta Amnion	Placenta Amnion
35	chr19:44671200-44681600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr19:44671200-44682200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
37	chr19:44671400-44677000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr19:44671400-44679000	Strong transcription	Brain Hippocampus Middle	brain
39	chr19:44671400-44682600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr19:44671800-44678600	Strong transcription	NHDF-Ad	bronchial
41	chr19:44672000-44681600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
42	chr19:44672000-44681800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
43	chr19:44673000-44676800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr19:44673000-44679800	Strong transcription	Fetal Brain Female	brain
45	chr19:44673200-44678000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
46	chr19:44673200-44678000	ZNF genes & repeats	Fetal Intestine Small	intestine
47	chr19:44673200-44680200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr19:44673400-44681400	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
49	chr19:44673600-44679800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr19:44673800-44678200	Strong transcription	H1 Cell Line	embryonic stem cell

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