Variant report

Variant	rs12554698
Chromosome Location	chr9:14641029-14641030
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10511594	0.88[CEU][hapmap];0.84[CHD][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs10738374	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10756596	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10756598	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10810201	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10810212	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs10961651	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs10961652	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs10961653	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs10961654	0.88[EUR][1000 genomes]
rs10961655	0.88[CEU][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs11790280	0.80[CEU][hapmap];0.85[TSI][hapmap]
rs12115353	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12551707	0.88[ASW][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.83[TSI][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12708257	0.84[CHB][hapmap]
rs13284172	0.84[CEU][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs13284901	0.88[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.91[EUR][1000 genomes]
rs13289971	1.00[CEU][hapmap];0.83[JPT][hapmap];0.93[EUR][1000 genomes]
rs13290219	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs13291396	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13296430	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs13299425	0.83[EUR][1000 genomes]
rs17288444	0.85[CHB][hapmap]
rs4469563	0.83[EUR][1000 genomes]
rs7849480	0.87[CHD][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7865184	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs7875420	0.88[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029491	chr9:14033607-14942373	Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv915804	chr9:14182608-14903050	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv831517	chr9:14512924-14738206	Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv613637	chr9:14524438-15011915	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv3362157	chr9:14542189-14791977	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv521363	chr9:14566406-14691897	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv892605	chr9:14585052-14709151	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv892606	chr9:14588049-14697022	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv892608	chr9:14589173-14689088	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv892609	chr9:14589173-14694302	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers 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	4 gene(s)	inside rSNPs	diseases
11	esv2752921	chr9:14593749-14694372	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	esv2755661	chr9:14615367-14660700	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv892610	chr9:14622952-14654900	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv892611	chr9:14635546-14676174	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv466260	chr9:14639666-14662459	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv613643	chr9:14639666-14662459	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:14595600-14653600	Weak transcription	NHDF-Ad	bronchial
2	chr9:14596600-14653600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr9:14597000-14655000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr9:14599800-14654000	Weak transcription	Fetal Heart	heart
5	chr9:14605600-14654800	Weak transcription	HSMM	muscle
6	chr9:14610200-14654800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr9:14612800-14641200	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr9:14613600-14654600	Weak transcription	Fetal Kidney	kidney
9	chr9:14617200-14646000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr9:14619400-14653600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr9:14619400-14654800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr9:14619600-14654800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr9:14626800-14655000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr9:14627800-14643400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr9:14629400-14654600	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr9:14629400-14655000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr9:14630000-14654400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr9:14630400-14654800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr9:14631000-14654000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr9:14631000-14654800	Weak transcription	Brain Anterior Caudate	brain
21	chr9:14631000-14654800	Weak transcription	Brain Hippocampus Middle	brain
22	chr9:14631000-14692400	Weak transcription	HSMMtube	muscle
23	chr9:14631200-14641200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr9:14631200-14653600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr9:14631200-14653600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr9:14631200-14653600	Weak transcription	Adipose Nuclei	Adipose
27	chr9:14631400-14653600	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr9:14631600-14653600	Weak transcription	Left Ventricle	heart
29	chr9:14631800-14654000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr9:14632200-14644600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr9:14632600-14654000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr9:14633400-14653800	Weak transcription	Fetal Lung	lung
33	chr9:14634200-14654000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr9:14634400-14653600	Weak transcription	Fetal Muscle Trunk	muscle
35	chr9:14634400-14654000	Weak transcription	Duodenum Mucosa	Duodenum
36	chr9:14634400-14686600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr9:14634600-14650800	Weak transcription	Esophagus	oesophagus
38	chr9:14634600-14651600	Weak transcription	Fetal Intestine Small	intestine
39	chr9:14634600-14654000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr9:14634600-14654200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr9:14634600-14654400	Weak transcription	Fetal Intestine Large	intestine
42	chr9:14634600-14654800	Weak transcription	Right Ventricle	heart
43	chr9:14634600-14659000	Weak transcription	Fetal Stomach	stomach
44	chr9:14634600-14692400	Weak transcription	Gastric	stomach
45	chr9:14634600-14692600	Weak transcription	Aorta	Aorta
46	chr9:14634800-14641200	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr9:14635600-14653800	Weak transcription	Brain Germinal Matrix	brain
48	chr9:14635800-14653600	Weak transcription	GM12878-XiMat	blood
49	chr9:14635800-14659800	Weak transcription	Ovary	ovary
50	chr9:14636000-14653600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links