Variant report

Variant	rs17658908
Chromosome Location	chr9:3294227-3294228
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs13283906	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs13286357	0.92[EUR][1000 genomes]
rs13288291	0.92[EUR][1000 genomes]
rs13299535	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs16917215	1.00[CEU][hapmap]
rs17659039	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17715422	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs34354121	0.83[EUR][1000 genomes]
rs34885235	0.92[EUR][1000 genomes]
rs35110056	0.88[EUR][1000 genomes]
rs35397020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35639292	0.94[EUR][1000 genomes]
rs36086495	0.88[EUR][1000 genomes]
rs7042345	0.82[CEU][hapmap]
rs7863972	0.89[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv466090	chr9:3237378-3349487	Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv613145	chr9:3237378-3349487	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1032529	chr9:3254763-3319778	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv539941	chr9:3254763-3319778	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	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
9	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17658908	TEX28///TEX28P1///TEX28P2	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:3234800-3294400	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr9:3244200-3338400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr9:3257200-3294400	Weak transcription	Duodenum Mucosa	Duodenum
4	chr9:3263200-3294600	Weak transcription	Esophagus	oesophagus
5	chr9:3263200-3297800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr9:3265600-3332000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr9:3272000-3302800	Weak transcription	Ovary	ovary
8	chr9:3275800-3294600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr9:3275800-3295600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr9:3276600-3295000	Weak transcription	Fetal Thymus	thymus
11	chr9:3276800-3299400	Weak transcription	Primary B cells from peripheral blood	blood
12	chr9:3277400-3310600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr9:3277400-3337400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr9:3286600-3296800	Weak transcription	Aorta	Aorta
15	chr9:3286600-3307000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr9:3287400-3295000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr9:3287600-3296400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr9:3288000-3305600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr9:3288200-3294400	Weak transcription	Adipose Nuclei	Adipose
20	chr9:3288200-3294800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr9:3288200-3294800	Weak transcription	Fetal Intestine Large	intestine
22	chr9:3288200-3296800	Weak transcription	Left Ventricle	heart
23	chr9:3288200-3309000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr9:3288200-3378400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr9:3288400-3299200	Weak transcription	Primary B cells from cord blood	blood
26	chr9:3288600-3318800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr9:3290200-3299600	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr9:3290600-3299200	Weak transcription	GM12878-XiMat	blood
29	chr9:3290800-3309200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr9:3291000-3294800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:3291000-3296800	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr9:3291000-3299000	Weak transcription	Fetal Brain Male	brain
33	chr9:3291400-3338600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr9:3291800-3318800	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr9:3292000-3300000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr9:3293200-3329600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr9:3293400-3295200	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr9:3293400-3299800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr9:3293400-3312800	Weak transcription	Primary T cells from cord blood	blood
40	chr9:3293400-3312800	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr9:3293400-3318800	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr9:3293600-3301400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr9:3293600-3352600	Weak transcription	Primary hematopoietic stem cells	blood
44	chr9:3294200-3294600	Enhancers	Primary monocytes fromperipheralblood	blood

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