Variant report

Variant	rs71356841
Chromosome Location	chr19:39648925-39648926
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	chr19:39615259..39630637-chr19:39640467..39653924,38	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269172	Chromatin interaction
ENSG00000130669	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1079442	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11083509	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11083510	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12610624	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12611361	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12611365	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12611376	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12984418	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17722300	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17795295	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2873913	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34058542	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34110379	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34270590	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34326918	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34808880	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34846983	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35163943	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35591784	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36148214	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3889485	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55748546	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61171111	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs67248178	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs71356838	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs71356839	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71356840	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs737450	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8107629	0.96[AMR][1000 genomes];0.93[EUR][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	nsv833829	chr19:39569681-39730777	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv432048	chr19:39572060-39850060	Bivalent/Poised TSS Bivalent Enhancer Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	esv3403825	chr19:39646612-39650810	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	3 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	chr19:39617400-39659800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr19:39630800-39651000	Weak transcription	NHDF-Ad	bronchial
3	chr19:39631000-39660000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr19:39636000-39668200	Weak transcription	Primary B cells from cord blood	blood
5	chr19:39636400-39665600	Weak transcription	Aorta	Aorta
6	chr19:39636800-39650800	Weak transcription	HUVEC	blood vessel
7	chr19:39637000-39653600	Weak transcription	Brain Germinal Matrix	brain
8	chr19:39637400-39660800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr19:39638000-39661400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr19:39640000-39672600	Weak transcription	GM12878-XiMat	blood
11	chr19:39640200-39660000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr19:39641200-39649200	Weak transcription	Fetal Brain Female	brain
13	chr19:39642000-39649600	Enhancers	Placenta	Placenta
14	chr19:39642400-39649000	Weak transcription	Thymus	Thymus
15	chr19:39644200-39652200	Enhancers	Placenta Amnion	Placenta Amnion
16	chr19:39644400-39649600	Enhancers	Pancreas	Pancrea
17	chr19:39644400-39651800	Genic enhancers	Fetal Intestine Small	intestine
18	chr19:39644600-39649000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr19:39644600-39649400	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr19:39644600-39649400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr19:39644600-39649400	Enhancers	Lung	lung
22	chr19:39644600-39649600	Enhancers	K562	blood
23	chr19:39644600-39649800	Enhancers	Fetal Intestine Large	intestine
24	chr19:39644600-39652200	Enhancers	Stomach Mucosa	stomach
25	chr19:39644800-39652400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr19:39645200-39659000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr19:39645400-39649600	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr19:39645400-39654600	Enhancers	Ovary	ovary
29	chr19:39645800-39658000	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr19:39646000-39649000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr19:39646000-39649000	Enhancers	Left Ventricle	heart
32	chr19:39646600-39649400	Enhancers	Right Ventricle	heart
33	chr19:39646600-39652200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr19:39646600-39653200	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr19:39646600-39659000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr19:39646800-39659200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr19:39646800-39660600	Weak transcription	Dnd41	blood
38	chr19:39647000-39649000	Enhancers	NH-A	brain
39	chr19:39647000-39649000	Flanking Active TSS	Osteobl	bone
40	chr19:39647000-39650400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr19:39647200-39649000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr19:39647200-39649400	Weak transcription	Primary T cells from cord blood	blood
43	chr19:39647200-39660400	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr19:39647400-39649000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr19:39647400-39649000	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr19:39647400-39649000	Enhancers	Rectal Smooth Muscle	rectum
47	chr19:39647400-39649000	Enhancers	Right Atrium	heart
48	chr19:39647400-39649200	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr19:39647400-39649400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr19:39647400-39651800	Genic enhancers	Spleen	Spleen

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