Variant report

Variant	rs12003940
Chromosome Location	chr9:19101350-19101351
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:19090764..19093304-chr9:19100948..19103618,2	K562	blood:
2	chr9:19098429..19101130-chr9:19101314..19102834,2	MCF-7	breast:
3	chr9:19100539..19103049-chr9:19229555..19232279,2	MCF-7	breast:
4	chr9:19048660..19050563-chr9:19101012..19103938,3	MCF-7	breast:
5	chr9:19101057..19103224-chr9:19126510..19128425,2	MCF-7	breast:
6	chr9:19100757..19103077-chr9:19112817..19114511,2	MCF-7	breast:
7	chr9:19078940..19081412-chr9:19100972..19102814,2	K562	blood:

Variant related genes	Relation type
ENSG00000155876	Chromatin interaction
ENSG00000137145	Chromatin interaction
ENSG00000147872	Chromatin interaction
ENSG00000147874	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs7855423	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7860122	0.84[ASN][1000 genomes]
rs9406758	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017820	chr9:18882219-19587377	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
2	nsv540078	chr9:18882219-19587377	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
3	nsv892700	chr9:18979441-19156784	Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv1028623	chr9:19034742-19394712	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv540079	chr9:19034742-19394712	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
6	nsv430003	chr9:19074740-19247826	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv870340	chr9:19077714-19143230	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv1018947	chr9:19094894-19394712	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	81 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	chr9:19051600-19101400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:19062000-19102200	Weak transcription	Stomach Mucosa	stomach
3	chr9:19077400-19102200	Weak transcription	Gastric	stomach
4	chr9:19086600-19102200	Weak transcription	Aorta	Aorta
5	chr9:19089600-19102000	Weak transcription	HSMMtube	muscle
6	chr9:19089800-19101800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr9:19091600-19102000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr9:19091800-19102000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:19093800-19101400	Weak transcription	Brain Angular Gyrus	brain
10	chr9:19093800-19101800	Weak transcription	Fetal Kidney	kidney
11	chr9:19093800-19102000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr9:19093800-19102200	Weak transcription	Brain Substantia Nigra	brain
13	chr9:19094800-19101400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr9:19096000-19101400	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr9:19096800-19101800	Weak transcription	NH-A	brain
16	chr9:19099600-19101400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr9:19099600-19101400	Strong transcription	Fetal Intestine Small	intestine
18	chr9:19099600-19101800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr9:19100200-19101400	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr9:19100200-19101600	Flanking Active TSS	Hela-S3	cervix
21	chr9:19100200-19101800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr9:19100200-19101800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr9:19100200-19102000	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr9:19100200-19102200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr9:19100400-19101600	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr9:19100400-19101800	Enhancers	Fetal Heart	heart
27	chr9:19100400-19102200	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr9:19100600-19101400	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr9:19100600-19101400	Flanking Active TSS	GM12878-XiMat	blood
30	chr9:19100600-19101400	Flanking Active TSS	HepG2	liver
31	chr9:19100600-19101600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:19100600-19101800	Enhancers	Primary T cells from cord blood	blood
33	chr9:19100600-19101800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr9:19100600-19101800	Enhancers	Brain Hippocampus Middle	brain
35	chr9:19100600-19101800	Enhancers	Monocytes-CD14+_RO01746	blood
36	chr9:19100600-19102200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr9:19100600-19103000	Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr9:19100800-19101400	Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr9:19100800-19101400	Transcr. at gene 5' and 3'	Dnd41	blood
40	chr9:19100800-19101600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr9:19100800-19101800	Enhancers	Primary hematopoietic stem cells	blood
42	chr9:19100800-19101800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr9:19100800-19101800	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr9:19100800-19101800	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr9:19100800-19101800	Enhancers	Small Intestine	intestine
46	chr9:19100800-19101800	Enhancers	NHDF-Ad	bronchial
47	chr9:19100800-19102000	Enhancers	Liver	Liver
48	chr9:19100800-19102000	Enhancers	Fetal Brain Male	brain
49	chr9:19100800-19103400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr9:19100800-19103400	Active TSS	iPS-20b Cell Line	embryonic stem cell

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