Variant report

Variant	rs1858999
Chromosome Location	chr19:19497669-19497670
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:19494550..19497983-chr19:19513188..19518336,8	MCF-7	breast:
2	chr19:19496697..19498287-chr19:19583016..19585062,2	MCF-7	breast:
3	chr19:18390819..18392505-chr19:19495105..19497896,2	K562	blood:
4	chr19:19494732..19500297-chr19:19512585..19520288,14	MCF-7	breast:
5	chr19:19491673..19504307-chr19:19513999..19523684,33	K562	blood:
6	chr19:19494923..19497823-chr19:19573798..19576950,3	K562	blood:
7	chr19:19497521..19500034-chr19:19556713..19558858,2	K562	blood:
8	chr19:19303122..19305309-chr19:19496096..19498095,2	K562	blood:
9	chr19:19489733..19491954-chr19:19497664..19499602,2	K562	blood:
10	chr19:19497354..19499230-chr19:19547808..19549334,2	K562	blood:
11	chr19:19496290..19497914-chr19:19774313..19776411,2	MCF-7	breast:
12	chr19:19492268..19501550-chr19:19512499..19523684,29	K562	blood:
13	chr19:19478626..19479419-chr19:19497318..19497870,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000105726	Chromatin interaction
ENSG00000130522	Chromatin interaction
ENSG00000064490	Chromatin interaction
ENSG00000267234	Chromatin interaction
ENSG00000167491	Chromatin interaction
ENSG00000254901	Chromatin interaction

Extended variants
information (count: 123 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs1000237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1009136	0.92[CEU][hapmap];0.85[JPT][hapmap];0.88[YRI][hapmap]
rs1010207	0.85[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs10282	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[ASN][1000 genomes]
rs10401193	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs10402308	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs10402451	0.87[AFR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10402627	0.87[ASN][1000 genomes]
rs10405625	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10410664	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10414830	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10419912	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10422819	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[ASN][1000 genomes]
rs1047361	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1054284	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap]
rs1054930	0.84[ASN][1000 genomes]
rs1063966	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11669516	0.92[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs12972397	0.94[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs12973258	0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs12975119	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12977524	0.94[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs13964	0.92[CEU][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap]
rs1469712	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1469713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs15622	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs17288409	0.90[ASN][1000 genomes]
rs1808653	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1865034	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2074088	0.87[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2074089	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs2074090	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs2074303	0.84[CEU][hapmap];0.80[JPT][hapmap];0.92[YRI][hapmap]
rs2074550	0.84[CEU][hapmap];0.80[JPT][hapmap];0.92[YRI][hapmap]
rs2099334	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2163804	0.94[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2163805	0.82[ASN][1000 genomes]
rs2269873	0.84[CEU][hapmap];0.80[JPT][hapmap];0.92[YRI][hapmap]
rs2285627	0.92[CEU][hapmap]
rs2288852	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2301784	0.84[CEU][hapmap];0.81[JPT][hapmap];0.92[YRI][hapmap]
rs2301786	0.85[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs2304098	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[ASN][1000 genomes]
rs2315025	0.86[JPT][hapmap]
rs2315279	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2315281	0.91[AFR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2315283	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2315610	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28478453	0.81[ASN][1000 genomes]
rs2905421	0.88[CEU][hapmap];1.00[YRI][hapmap]
rs2905424	0.92[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs2905425	0.92[CEU][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs2905430	0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2905431	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2905432	0.86[EUR][1000 genomes]
rs2905435	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2916069	0.94[AFR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2916073	0.94[AFR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2916074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2916076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2965175	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2965180	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2965182	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2965183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2965185	1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs2965188	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2965189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2965193	0.88[CEU][hapmap];1.00[YRI][hapmap]
rs2965198	0.92[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs2965199	0.84[EUR][1000 genomes]
rs34277109	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34538000	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34647936	0.82[ASN][1000 genomes]
rs35418933	0.94[AFR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3752151	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap]
rs3764567	0.88[CEU][hapmap]
rs3794990	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3794993	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4808198	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4808199	0.94[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs4808200	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4808202	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4808203	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4808208	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[ASN][1000 genomes]
rs4808931	0.84[YRI][hapmap]
rs4808950	0.87[ASN][1000 genomes]
rs4808955	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4808957	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4808959	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4808960	0.94[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs4808961	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4808964	0.88[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs4808965	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[ASN][1000 genomes]
rs4808967	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[ASN][1000 genomes]
rs60003758	0.82[ASN][1000 genomes]
rs60321073	0.90[ASN][1000 genomes]
rs6511026	0.84[CEU][hapmap];0.80[JPT][hapmap];0.92[YRI][hapmap]
rs6511036	0.94[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs6511038	0.86[AFR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6909	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[ASN][1000 genomes]
rs7245983	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs7250893	0.86[ASN][1000 genomes]
rs7252888	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs7253807	0.84[ASN][1000 genomes]
rs7254230	0.92[CEU][hapmap];0.86[JPT][hapmap]
rs7254748	0.85[CEU][hapmap];1.00[YRI][hapmap]
rs7256149	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs735273	0.84[CEU][hapmap];0.80[JPT][hapmap];0.92[YRI][hapmap]
rs747050	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs751856	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs751858	0.86[ASN][1000 genomes]
rs754255	0.82[ASN][1000 genomes]
rs769267	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs8101499	0.82[ASN][1000 genomes]
rs8103197	0.92[CEU][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap]
rs8103496	0.84[CEU][hapmap];0.80[JPT][hapmap];0.92[YRI][hapmap]
rs8108647	0.85[JPT][hapmap]
rs892021	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs892022	0.89[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap]
rs9917108	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.89[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	nsv911303	chr19:19256870-19505087	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv1056419	chr19:19421218-19510611	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19495400-19497800	Active TSS	H9 Cell Line	embryonic stem cell
2	chr19:19495400-19498200	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr19:19495400-19498400	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr19:19495600-19497800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr19:19495600-19497800	Active TSS	HSMM	muscle
6	chr19:19495600-19498000	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr19:19495600-19498000	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr19:19495800-19497800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:19495800-19497800	Active TSS	Aorta	Aorta
10	chr19:19495800-19497800	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr19:19495800-19497800	Active TSS	Fetal Kidney	kidney
12	chr19:19495800-19497800	Active TSS	Placenta Amnion	Placenta Amnion
13	chr19:19495800-19498000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr19:19495800-19498000	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr19:19496000-19497800	Active TSS	GM12878-XiMat	blood
16	chr19:19496000-19497800	Active TSS	NHDF-Ad	bronchial
17	chr19:19496200-19498000	Active TSS	Lung	lung
18	chr19:19496800-19498400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
19	chr19:19497000-19497800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr19:19497000-19497800	Flanking Active TSS	Brain Cingulate Gyrus	brain
21	chr19:19497000-19497800	Flanking Active TSS	Fetal Muscle Trunk	muscle
22	chr19:19497000-19498000	Flanking Active TSS	Primary B cells from peripheral blood	blood
23	chr19:19497000-19498000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
24	chr19:19497000-19498000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
25	chr19:19497000-19498000	Enhancers	Fetal Brain Male	brain
26	chr19:19497000-19498000	Flanking Active TSS	Fetal Muscle Leg	muscle
27	chr19:19497000-19498000	Flanking Active TSS	Placenta	Placenta
28	chr19:19497000-19498000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
29	chr19:19497000-19498000	Flanking Active TSS	Stomach Smooth Muscle	stomach
30	chr19:19497000-19498200	Flanking Active TSS	Primary hematopoietic stem cells	blood
31	chr19:19497000-19498200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr19:19497200-19497800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr19:19497200-19497800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr19:19497200-19497800	Flanking Active TSS	Liver	Liver
35	chr19:19497200-19497800	Flanking Active TSS	Brain Germinal Matrix	brain
36	chr19:19497200-19497800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr19:19497200-19498000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr19:19497200-19498000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr19:19497200-19498000	Flanking Active TSS	Primary B cells from cord blood	blood
40	chr19:19497200-19498000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
41	chr19:19497200-19498000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr19:19497200-19498000	Flanking Active TSS	Brain Anterior Caudate	brain
43	chr19:19497200-19498000	Flanking Active TSS	Brain Hippocampus Middle	brain
44	chr19:19497200-19498000	Flanking Active TSS	Colonic Mucosa	Colon
45	chr19:19497200-19498000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr19:19497200-19498000	Flanking Active TSS	Fetal Brain Female	brain
47	chr19:19497200-19498000	Flanking Active TSS	Psoas Muscle	Psoas
48	chr19:19497200-19498000	Flanking Active TSS	Rectal Smooth Muscle	rectum
49	chr19:19497200-19498000	Flanking Active TSS	Right Ventricle	heart
50	chr19:19497200-19498000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links