Variant report

Variant	rs17255321
Chromosome Location	chr1:184560541-184560542
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10489723	1.00[CEU][hapmap]
rs10911611	1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs16823145	0.88[MEX][hapmap]
rs16823336	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs16823340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16823344	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.88[MEX][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1832552	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2207521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55699645	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56691746	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56715278	0.84[EUR][1000 genomes]
rs60220474	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6695258	0.88[MEX][hapmap]
rs6698504	0.88[MEX][hapmap]
rs6701227	0.87[CHD][hapmap]
rs7520438	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7520700	0.89[ASN][1000 genomes]
rs7528356	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530079	chr1:183797938-184639971	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv2756618	chr1:184393343-184674343	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17255321	TMEM79	trans	brain	seeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184546200-184563800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:184546200-184566600	Weak transcription	Left Ventricle	heart
3	chr1:184547800-184580000	Weak transcription	Colon Smooth Muscle	Colon
4	chr1:184549400-184564600	Weak transcription	NHDF-Ad	bronchial
5	chr1:184553200-184566200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:184553200-184566600	Weak transcription	Fetal Stomach	stomach
7	chr1:184553600-184566200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:184553600-184566200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:184555400-184561800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:184557000-184566400	Weak transcription	Psoas Muscle	Psoas
11	chr1:184557000-184566400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr1:184557200-184566400	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr1:184557200-184574000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr1:184557200-184591600	Weak transcription	Aorta	Aorta
15	chr1:184558000-184560600	Enhancers	Fetal Intestine Large	intestine
16	chr1:184558000-184560600	Enhancers	Fetal Intestine Small	intestine
17	chr1:184558400-184561800	Weak transcription	A549	lung
18	chr1:184558600-184564600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:184558600-184564800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:184558600-184566400	Weak transcription	Fetal Muscle Leg	muscle
21	chr1:184558600-184568000	Weak transcription	Pancreas	Pancrea
22	chr1:184558600-184572600	Weak transcription	Lung	lung
23	chr1:184558800-184566600	Weak transcription	Fetal Lung	lung
24	chr1:184559000-184588400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:184559200-184562000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr1:184559200-184564400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:184559200-184564800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:184559200-184566600	Weak transcription	Right Ventricle	heart
29	chr1:184559200-184580400	Weak transcription	Adipose Nuclei	Adipose
30	chr1:184559400-184580400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr1:184559600-184563600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr1:184559600-184564600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:184559600-184564800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:184559600-184565000	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr1:184559600-184578000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:184559800-184560800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:184559800-184561600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr1:184559800-184561800	Weak transcription	Duodenum Mucosa	Duodenum
39	chr1:184559800-184563400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr1:184559800-184564200	Weak transcription	NHEK	skin
41	chr1:184559800-184564800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr1:184559800-184566200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:184559800-184566400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr1:184560000-184562000	Weak transcription	Placenta	Placenta
45	chr1:184560000-184564800	Weak transcription	HMEC	breast
46	chr1:184560200-184566600	Weak transcription	Liver	Liver
47	chr1:184560400-184562400	Weak transcription	Stomach Mucosa	stomach
48	chr1:184560400-184564600	Weak transcription	HSMM	muscle
49	chr1:184560400-184565600	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr1:184560400-184566400	Weak transcription	Rectal Mucosa Donor 29	rectum

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