Variant report

Variant	rs12004091
Chromosome Location	chr9:6521924-6521925
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:6516849..6518888-chr9:6521453..6523458,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10815460	1.00[AMR][1000 genomes]
rs10975706	1.00[AMR][1000 genomes]
rs10975713	1.00[AMR][1000 genomes]
rs12005111	1.00[AMR][1000 genomes]
rs12339217	1.00[AMR][1000 genomes]
rs13302691	0.89[ASN][1000 genomes]
rs28626232	1.00[AMR][1000 genomes]
rs55872463	1.00[AMR][1000 genomes]
rs60151754	1.00[AMR][1000 genomes]
rs60798406	1.00[AMR][1000 genomes]
rs73639310	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv933124	chr9:6099101-6644738	Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv1029000	chr9:6188652-6687205	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
5	nsv1031459	chr9:6216913-6657192	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv948562	chr9:6222553-6684955	Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	nsv1032350	chr9:6328167-6630686	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv892161	chr9:6364449-6523056	Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv831497	chr9:6377501-6612402	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
10	nsv1029766	chr9:6437020-6523605	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
11	nsv892162	chr9:6480005-6788085	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
12	nsv831498	chr9:6496021-6689728	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
13	esv2761298	chr9:6505897-6544766	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
14	nsv934176	chr9:6517535-6644738	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	esv2761484	chr9:6518374-6527209	Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6498800-6554400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr9:6499000-6528400	Weak transcription	Pancreas	Pancrea
3	chr9:6506400-6530600	Weak transcription	Gastric	stomach
4	chr9:6507000-6523800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr9:6507000-6524800	Weak transcription	Brain Hippocampus Middle	brain
6	chr9:6507000-6534400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr9:6507200-6522400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr9:6508400-6523600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr9:6508400-6525000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr9:6508400-6526400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr9:6508400-6526600	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr9:6508400-6528200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:6508400-6530600	Weak transcription	Left Ventricle	heart
14	chr9:6508600-6524200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr9:6508600-6537800	Weak transcription	HMEC	breast
16	chr9:6508600-6538200	Weak transcription	NHEK	skin
17	chr9:6508800-6523800	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr9:6508800-6526600	Weak transcription	HSMM	muscle
19	chr9:6509800-6525000	Weak transcription	Osteobl	bone
20	chr9:6509800-6530200	Weak transcription	A549	lung
21	chr9:6510400-6558800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr9:6510600-6522200	Weak transcription	NHDF-Ad	bronchial
23	chr9:6510600-6525000	Weak transcription	NH-A	brain
24	chr9:6510600-6543000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr9:6511400-6526800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr9:6512200-6525000	Weak transcription	HSMMtube	muscle
27	chr9:6512200-6528800	Weak transcription	NHLF	lung
28	chr9:6517600-6528000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:6518000-6526000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr9:6518000-6530400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr9:6518200-6526000	Weak transcription	Fetal Thymus	thymus
32	chr9:6518400-6525000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr9:6519000-6522200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr9:6520600-6522000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr9:6521200-6522000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr9:6521200-6522800	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr9:6521200-6523000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr9:6521200-6523200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
39	chr9:6521600-6522000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr9:6521600-6522000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr9:6521600-6522200	ZNF genes & repeats	Fetal Brain Male	brain
42	chr9:6521600-6524000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr9:6521600-6524200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr9:6521800-6522000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
45	chr9:6521800-6522000	ZNF genes & repeats	Fetal Stomach	stomach
46	chr9:6521800-6522000	ZNF genes & repeats	Thymus	Thymus
47	chr9:6521800-6522400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr9:6521800-6522400	ZNF genes & repeats	GM12878-XiMat	blood
49	chr9:6521800-6522600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr9:6521800-6523000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links