Variant report

Variant	rs12339196
Chromosome Location	chr9:6563418-6563419
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:6562859..6565330-chr9:6565433..6569047,3	K562	blood:
2	chr9:6550978..6552657-chr9:6561789..6563568,2	K562	blood:

Variant related genes	Relation type
ENSG00000237158	Chromatin interaction
ENSG00000252110	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10975645	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs10975646	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs10975647	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs12349059	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs28404672	0.94[AFR][1000 genomes]
rs9299033	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 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	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
9	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
10	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
11	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
12	nsv892163	chr9:6523056-6632061	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv1025627	chr9:6523056-6648098	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	esv2752308	chr9:6523060-6899149	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
15	nsv613206	chr9:6525753-6686738	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
16	esv3324686	chr9:6528411-6728310	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
17	nsv1028402	chr9:6542253-6874231	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
18	nsv1018308	chr9:6544766-6869653	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
19	nsv1015462	chr9:6544766-6874231	Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
20	nsv1018870	chr9:6548393-6708345	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
21	nsv892164	chr9:6555079-6664282	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
22	nsv931094	chr9:6558442-6672439	ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6532000-6570400	Strong transcription	Liver	Liver
2	chr9:6554600-6568600	Weak transcription	Fetal Intestine Small	intestine
3	chr9:6556000-6566800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr9:6557000-6564600	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr9:6558400-6564600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr9:6558600-6564600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:6558600-6564600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr9:6558600-6567000	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr9:6558600-6586600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr9:6558800-6580800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr9:6559200-6583400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr9:6559600-6568200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr9:6559800-6567600	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr9:6560200-6569400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr9:6560200-6572200	Weak transcription	GM12878-XiMat	blood
16	chr9:6560400-6565800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr9:6561200-6564400	Weak transcription	Right Atrium	heart
18	chr9:6561200-6591000	Weak transcription	Placenta	Placenta
19	chr9:6561600-6566800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr9:6561600-6566800	Enhancers	HUVEC	blood vessel
21	chr9:6561800-6564400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr9:6561800-6566800	Enhancers	Muscle Satellite Cultured Cells	--
23	chr9:6562400-6564400	Weak transcription	HepG2	liver
24	chr9:6562800-6563600	Enhancers	Hela-S3	cervix
25	chr9:6562800-6563800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr9:6562800-6565400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr9:6562800-6565600	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr9:6562800-6566800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr9:6563000-6563600	Enhancers	NH-A	brain
30	chr9:6563000-6563600	Enhancers	NHEK	skin
31	chr9:6563000-6563800	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr9:6563000-6563800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr9:6563000-6564600	Weak transcription	HSMM	muscle
34	chr9:6563000-6565000	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr9:6563000-6566400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr9:6563000-6566800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr9:6563000-6566800	Enhancers	Osteobl	bone
38	chr9:6563000-6567000	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr9:6563000-6567400	Strong transcription	H9 Cell Line	embryonic stem cell
40	chr9:6563200-6563600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr9:6563200-6563800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr9:6563200-6563800	Genic enhancers	A549	lung
43	chr9:6563200-6564400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr9:6563200-6564800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr9:6563400-6563600	Enhancers	Fetal Muscle Trunk	muscle
46	chr9:6563400-6563600	Enhancers	HSMMtube	muscle
47	chr9:6563400-6564400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr9:6563400-6564400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr9:6563400-6564400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr9:6563400-6564400	Weak transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links