Variant report

Variant	rs7254914
Chromosome Location	chr19:40315841-40315842
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39900714..39902326-chr19:40314340..40316336,2	MCF-7	breast:
2	chr19:40314923..40317084-chr19:40321250..40326069,8	MCF-7	breast:
3	chr19:40305000..40306597-chr19:40314975..40317382,2	K562	blood:
4	chr19:40301803..40305513-chr19:40314560..40316955,3	MCF-7	breast:
5	chr19:40296262..40298626-chr19:40313380..40316915,4	MCF-7	breast:
6	chr19:40313245..40319369-chr19:40333328..40340168,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105202	Chromatin interaction
ENSG00000105204	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10422280	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11880094	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11880956	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11883249	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12980289	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2072290	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2354800	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3810383	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3810386	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803297	0.96[ASN][1000 genomes]
rs616650	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs619350	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62106867	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508912	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6508913	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs718066	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246501	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7248926	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7253739	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258351	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3329492	chr19:40198535-40437035	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2758498	chr19:40227904-40521130	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv2758760	chr19:40227904-40521130	Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv428022	chr19:40227904-40521130	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
5	nsv911696	chr19:40310497-40344648	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv9725	chr19:40315519-40412523	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40312000-40323200	Strong transcription	A549	lung
2	chr19:40312200-40316800	Weak transcription	Hela-S3	cervix
3	chr19:40313600-40320200	Weak transcription	K562	blood
4	chr19:40314200-40316000	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr19:40314600-40316000	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr19:40314600-40316000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr19:40315200-40316200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:40315200-40316200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr19:40315200-40316200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr19:40315200-40316200	Enhancers	Stomach Mucosa	stomach
11	chr19:40315200-40316400	Enhancers	Fetal Heart	heart
12	chr19:40315200-40316400	Weak transcription	Left Ventricle	heart
13	chr19:40315200-40319200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr19:40315200-40320400	Weak transcription	Aorta	Aorta
15	chr19:40315200-40320400	Weak transcription	Psoas Muscle	Psoas
16	chr19:40315400-40316000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr19:40315400-40316000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr19:40315400-40316000	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr19:40315400-40316000	Enhancers	Primary B cells from peripheral blood	blood
20	chr19:40315400-40316000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr19:40315400-40316000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr19:40315400-40316000	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr19:40315400-40316000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr19:40315400-40316000	Flanking Active TSS	Brain Angular Gyrus	brain
25	chr19:40315400-40316000	Flanking Active TSS	Brain Hippocampus Middle	brain
26	chr19:40315400-40316000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr19:40315400-40316000	Enhancers	Colon Smooth Muscle	Colon
28	chr19:40315400-40316000	Enhancers	Gastric	stomach
29	chr19:40315400-40316000	Weak transcription	Lung	lung
30	chr19:40315400-40316000	Enhancers	Spleen	Spleen
31	chr19:40315400-40316000	Flanking Active TSS	Dnd41	blood
32	chr19:40315400-40316200	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr19:40315400-40316200	Enhancers	Pancreas	Pancrea
34	chr19:40315400-40316600	Weak transcription	Ovary	ovary
35	chr19:40315400-40316800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr19:40315400-40319400	Weak transcription	HSMM	muscle
37	chr19:40315400-40322800	Strong transcription	Placenta	Placenta
38	chr19:40315600-40316000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr19:40315600-40316000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr19:40315600-40316000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr19:40315600-40316000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr19:40315600-40316000	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr19:40315600-40316000	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr19:40315600-40316000	Flanking Active TSS	Brain Germinal Matrix	brain
45	chr19:40315600-40316000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr19:40315600-40316000	Enhancers	Fetal Lung	lung
47	chr19:40315600-40316000	Enhancers	Fetal Thymus	thymus
48	chr19:40315600-40316000	Enhancers	Right Ventricle	heart
49	chr19:40315600-40316000	Flanking Active TSS	Stomach Smooth Muscle	stomach
50	chr19:40315600-40316000	Enhancers	GM12878-XiMat	blood

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