Variant report

Variant	rs12555502
Chromosome Location	chr9:93606831-93606832
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11787537	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs12004706	0.86[ASN][1000 genomes]
rs17489214	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35758162	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56222210	0.86[ASN][1000 genomes]
rs62559143	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62559145	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62559146	1.00[ASN][1000 genomes]
rs7030222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72729051	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7855964	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046989	chr9:93353987-93800416	Transcr. at gene 5' and 3' Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv893567	chr9:93519280-93609668	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv831652	chr9:93527411-93696923	Bivalent Enhancer Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv893568	chr9:93539879-93774385	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1038685	chr9:93556174-93685729	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1039761	chr9:93598856-93677831	Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1039326	chr9:93598856-93685729	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:93565000-93609000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr9:93585600-93607800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr9:93596000-93607600	Weak transcription	Fetal Intestine Large	intestine
4	chr9:93599200-93616600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:93600200-93613800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr9:93601800-93642200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr9:93602600-93609200	Weak transcription	Right Ventricle	heart
8	chr9:93604400-93616200	Weak transcription	HMEC	breast
9	chr9:93604800-93612400	Weak transcription	Placenta	Placenta
10	chr9:93604800-93616600	Weak transcription	NHEK	skin
11	chr9:93604800-93617200	Strong transcription	Spleen	Spleen
12	chr9:93605000-93616400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr9:93605000-93622800	Weak transcription	Adipose Nuclei	Adipose
14	chr9:93605000-93633000	Weak transcription	Fetal Kidney	kidney
15	chr9:93605200-93608200	Strong transcription	Pancreas	Pancrea
16	chr9:93605200-93616400	Weak transcription	K562	blood
17	chr9:93605400-93612400	Strong transcription	Gastric	stomach
18	chr9:93605400-93614200	Strong transcription	Fetal Stomach	stomach
19	chr9:93605600-93608400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr9:93605600-93612600	Strong transcription	GM12878-XiMat	blood
21	chr9:93605600-93615600	Strong transcription	Duodenum Mucosa	Duodenum
22	chr9:93605600-93617400	Strong transcription	Thymus	Thymus
23	chr9:93605800-93607000	Weak transcription	Primary B cells from cord blood	blood
24	chr9:93605800-93621400	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr9:93605800-93621600	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr9:93605800-93631000	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr9:93606000-93608200	Strong transcription	Colonic Mucosa	Colon
28	chr9:93606000-93615600	Strong transcription	Fetal Thymus	thymus
29	chr9:93606000-93616600	Strong transcription	Fetal Intestine Small	intestine
30	chr9:93606000-93619600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr9:93606200-93612000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr9:93606200-93615600	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr9:93606200-93615600	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr9:93606200-93616200	Strong transcription	Primary B cells from peripheral blood	blood
35	chr9:93606200-93616400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr9:93606200-93616800	Strong transcription	Primary hematopoietic stem cells	blood
37	chr9:93606400-93616200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr9:93606400-93616400	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr9:93606600-93607800	Weak transcription	Esophagus	oesophagus
40	chr9:93606600-93609000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr9:93606600-93610400	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr9:93606600-93611200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr9:93606600-93611200	Strong transcription	Stomach Mucosa	stomach
44	chr9:93606600-93615000	Weak transcription	Liver	Liver
45	chr9:93606600-93615600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr9:93606600-93617400	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr9:93606600-93619200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr9:93606800-93609400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr9:93606800-93609800	Weak transcription	Lung	lung

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