Variant report

Variant	rs2168989
Chromosome Location	chr19:44712684-44712685
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:44711494..44713254-chr19:45003869..45006588,2	MCF-7	breast:
2	chr19:44709921..44713618-chr19:44714834..44717350,4	K562	blood:
3	chr19:44710790..44713844-chr19:44714955..44718823,7	MCF-7	breast:
4	chr19:44711481..44713542-chr19:44808275..44810056,2	K562	blood:

Variant related genes	Relation type
ENSG00000159917	Chromatin interaction
ENSG00000131115	Chromatin interaction
ENSG00000167384	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10405450	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10410086	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10423306	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10425945	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11666199	0.84[EUR][1000 genomes]
rs11667521	0.85[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap]
rs12459795	0.86[EUR][1000 genomes]
rs12460039	0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12462557	0.85[CEU][hapmap];0.92[GIH][hapmap];0.86[TSI][hapmap]
rs12462723	0.85[CEU][hapmap];0.92[GIH][hapmap];0.86[TSI][hapmap]
rs12608984	0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs12972784	0.90[EUR][1000 genomes]
rs12975546	0.85[CEU][hapmap]
rs12980565	0.85[CEU][hapmap]
rs2051059	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs2085516	0.86[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2100643	0.86[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2125579	0.85[CEU][hapmap];0.85[GIH][hapmap];0.86[TSI][hapmap]
rs2232801	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];0.95[GIH][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2279073	0.85[CEU][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap]
rs2293587	0.82[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.86[ASN][1000 genomes]
rs2356751	0.86[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.86[ASN][1000 genomes]
rs3817595	0.86[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.86[ASN][1000 genomes]
rs4802218	0.84[CEU][hapmap]
rs56357907	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs58778698	0.86[ASN][1000 genomes]
rs60668498	0.80[ASN][1000 genomes]
rs61412562	0.83[ASN][1000 genomes]
rs61589395	0.83[ASN][1000 genomes]
rs62117770	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6509146	0.86[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7248114	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7249209	0.86[CHB][hapmap];0.83[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7251682	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7253196	0.87[EUR][1000 genomes]
rs7253533	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7259916	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7260304	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8101032	0.85[CEU][hapmap]
rs8102037	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8105073	0.87[CEU][hapmap]
rs8108934	0.83[EUR][1000 genomes]
rs9304640	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9646643	0.85[CEU][hapmap];0.95[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
rs2168989	SIGLEC16	cis	cerebellum	SCAN
rs2168989	SAE1	cis	cerebellum	SCAN
rs2168989	SIX5	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44710400-44713400	Active TSS	Duodenum Smooth Muscle	Duodenum
2	chr19:44711200-44712800	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr19:44711200-44712800	Active TSS	Brain Anterior Caudate	brain
4	chr19:44711200-44712800	Active TSS	Psoas Muscle	Psoas
5	chr19:44711200-44712800	Active TSS	Right Atrium	heart
6	chr19:44711200-44712800	Active TSS	HSMMtube	muscle
7	chr19:44711200-44713000	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr19:44711200-44713200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:44711200-44713200	Active TSS	Rectal Mucosa Donor 31	rectum
10	chr19:44711200-44713200	Active TSS	Skeletal Muscle Male	skeletal muscle
11	chr19:44711200-44713200	Active TSS	K562	blood
12	chr19:44711800-44712800	Flanking Active TSS	Liver	Liver
13	chr19:44712000-44712800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr19:44712200-44712800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
15	chr19:44712200-44712800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
16	chr19:44712200-44712800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
17	chr19:44712200-44712800	Enhancers	Hela-S3	cervix
18	chr19:44712200-44713000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr19:44712200-44713000	Flanking Active TSS	Dnd41	blood
20	chr19:44712200-44716000	Weak transcription	Primary B cells from peripheral blood	blood
21	chr19:44712200-44716000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr19:44712200-44716000	Weak transcription	Fetal Muscle Trunk	muscle
23	chr19:44712200-44716000	Weak transcription	Left Ventricle	heart
24	chr19:44712200-44716200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr19:44712200-44716200	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr19:44712200-44716200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr19:44712200-44716200	Weak transcription	Brain Substantia Nigra	brain
28	chr19:44712200-44716600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr19:44712400-44712800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr19:44712400-44712800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr19:44712400-44712800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr19:44712400-44712800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr19:44712400-44712800	Enhancers	Muscle Satellite Cultured Cells	--
34	chr19:44712400-44712800	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr19:44712400-44712800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr19:44712400-44712800	Enhancers	Brain Cingulate Gyrus	brain
37	chr19:44712400-44712800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr19:44712400-44712800	Active TSS	Fetal Brain Male	brain
39	chr19:44712400-44712800	Weak transcription	NHDF-Ad	bronchial
40	chr19:44712400-44713000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr19:44712400-44713000	Enhancers	Primary T cells from cord blood	blood
42	chr19:44712400-44713000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr19:44712400-44715800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr19:44712400-44716000	Weak transcription	Brain Hippocampus Middle	brain
45	chr19:44712400-44716200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr19:44712400-44716200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr19:44712400-44716200	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr19:44712400-44716200	Weak transcription	Duodenum Mucosa	Duodenum
49	chr19:44712400-44716200	Weak transcription	Fetal Brain Female	brain
50	chr19:44712400-44716200	Weak transcription	HUVEC	blood vessel

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