Variant report

Variant	rs12553270
Chromosome Location	chr9:3393348-3393349
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10113980	1.00[YRI][hapmap]
rs10114162	0.87[CEU][hapmap];0.83[CHB][hapmap]
rs10114838	0.87[CEU][hapmap];0.83[CHB][hapmap]
rs10115578	0.87[CEU][hapmap];0.82[CHB][hapmap]
rs10119982	0.87[CEU][hapmap]
rs10121096	0.85[CEU][hapmap]
rs10814189	0.83[CHB][hapmap]
rs10814190	0.82[CHB][hapmap]
rs10971734	0.83[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs10971975	0.83[EUR][1000 genomes]
rs12004862	0.87[CEU][hapmap];0.82[CHB][hapmap]
rs12238307	0.87[CEU][hapmap];0.82[CHB][hapmap]
rs12340274	0.86[CEU][hapmap];0.82[CHB][hapmap]
rs12353393	0.85[CEU][hapmap]
rs1342542	0.87[CEU][hapmap];0.83[CHB][hapmap]
rs16917918	0.81[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs34700106	0.85[ASN][1000 genomes]
rs3739461	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs7026025	0.87[CEU][hapmap];0.82[CHB][hapmap]
rs7857554	0.87[CEU][hapmap];0.83[CHB][hapmap]
rs7861625	0.87[CEU][hapmap];0.83[CHB][hapmap]
rs881167	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892086	chr9:3012276-3410838	Bivalent Enhancer ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1032921	chr9:3139007-3502815	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv539940	chr9:3139007-3502815	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv531566	chr9:3288211-3545454	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv892089	chr9:3290569-3578094	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv916259	chr9:3308176-4296711	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv1034280	chr9:3319718-3491987	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv539942	chr9:3319718-3491987	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1028815	chr9:3319718-3584455	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
10	nsv613147	chr9:3368111-3440355	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	esv1849738	chr9:3389223-3404434	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
12	nsv892090	chr9:3391364-3496660	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3341200-3397600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr9:3351000-3408200	Weak transcription	Fetal Intestine Small	intestine
3	chr9:3364200-3397200	Weak transcription	Left Ventricle	heart
4	chr9:3364800-3393800	Weak transcription	Adipose Nuclei	Adipose
5	chr9:3369400-3398400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr9:3377600-3401400	Weak transcription	HMEC	breast
7	chr9:3377800-3401600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr9:3381000-3397000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr9:3382200-3425000	Weak transcription	Aorta	Aorta
10	chr9:3382400-3397000	Weak transcription	Fetal Intestine Large	intestine
11	chr9:3382400-3401400	Weak transcription	Brain Anterior Caudate	brain
12	chr9:3382800-3401000	Weak transcription	Brain Germinal Matrix	brain
13	chr9:3383200-3410000	Weak transcription	Fetal Brain Male	brain
14	chr9:3383400-3401400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr9:3385200-3395800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr9:3386000-3398000	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr9:3386200-3409600	Weak transcription	Psoas Muscle	Psoas
18	chr9:3387000-3397200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr9:3387200-3393400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr9:3387200-3394600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr9:3387200-3397000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr9:3387200-3397000	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr9:3387200-3401000	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr9:3387200-3433800	Weak transcription	Pancreas	Pancrea
25	chr9:3387600-3397600	Weak transcription	HepG2	liver
26	chr9:3387800-3401400	Weak transcription	Brain Hippocampus Middle	brain
27	chr9:3388000-3401400	Weak transcription	Brain Cingulate Gyrus	brain
28	chr9:3388200-3401400	Weak transcription	Brain Substantia Nigra	brain
29	chr9:3388600-3394400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr9:3388600-3397600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr9:3388600-3401800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr9:3388800-3395000	Weak transcription	Fetal Thymus	thymus
33	chr9:3388800-3395800	Weak transcription	Lung	lung
34	chr9:3388800-3397800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr9:3388800-3401800	Weak transcription	Fetal Stomach	stomach
36	chr9:3389200-3394800	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr9:3389200-3395400	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr9:3389200-3398600	Weak transcription	Spleen	Spleen
39	chr9:3390400-3397200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr9:3390600-3398600	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr9:3390600-3398600	Weak transcription	Thymus	Thymus
42	chr9:3390800-3396000	Weak transcription	Ovary	ovary
43	chr9:3390800-3396800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr9:3390800-3397000	Weak transcription	Fetal Muscle Leg	muscle
45	chr9:3390800-3398400	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr9:3390800-3401200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr9:3390800-3401600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr9:3391000-3401800	Weak transcription	Duodenum Mucosa	Duodenum
49	chr9:3391200-3397000	Weak transcription	Primary hematopoietic stem cells	blood
50	chr9:3391400-3395400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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