Variant report

Variant	rs7556011
Chromosome Location	chr1:179105110-179105111
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10913690	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10913695	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10913697	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12130276	0.85[EUR][1000 genomes]
rs1325195	0.82[ASN][1000 genomes]
rs1856967	0.83[EUR][1000 genomes]
rs1856968	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1858551	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2087559	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2171959	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2258217	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2258221	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2486995	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2486997	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2493124	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2636274	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2636276	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2636280	0.83[EUR][1000 genomes]
rs2636287	0.85[EUR][1000 genomes]
rs2791940	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2791941	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2791943	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2793793	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2793794	0.81[ASN][1000 genomes]
rs2793795	0.80[ASN][1000 genomes]
rs2793796	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2793797	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2793798	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2793812	0.83[EUR][1000 genomes]
rs2816183	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2816185	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2816186	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2816187	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2816189	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2816196	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2816197	0.81[EUR][1000 genomes]
rs2816198	0.83[EUR][1000 genomes]
rs2816199	0.83[EUR][1000 genomes]
rs2816202	0.83[EUR][1000 genomes]
rs2816203	0.83[EUR][1000 genomes]
rs2816204	0.83[EUR][1000 genomes]
rs3210839	0.81[EUR][1000 genomes]
rs36122838	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3813642	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3813643	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4651012	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4651013	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs965401	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9726961	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9727252	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9728480	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9729199	0.83[EUR][1000 genomes];0.81[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	nsv1012667	chr1:179094571-179120280	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1002253	chr1:179094571-179120938	Strong transcription Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1001191	chr1:179097246-179120938	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv3423413	chr1:179103954-179106502	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7556011	TOR3A	cis	Artery Tibial	GTEx

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179063200-179112000	Weak transcription	Fetal Kidney	kidney
2	chr1:179079600-179109800	Weak transcription	Small Intestine	intestine
3	chr1:179087800-179113000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:179091000-179108800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:179091000-179109000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:179091000-179109200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:179093400-179117200	Weak transcription	Fetal Stomach	stomach
8	chr1:179095800-179106800	Weak transcription	Gastric	stomach
9	chr1:179095800-179107400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr1:179096400-179108800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:179096600-179106800	Weak transcription	Fetal Lung	lung
12	chr1:179096600-179110200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr1:179098200-179112000	Weak transcription	Lung	lung
14	chr1:179099200-179110200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr1:179099200-179110400	Weak transcription	Brain Angular Gyrus	brain
16	chr1:179099200-179110400	Weak transcription	Brain Anterior Caudate	brain
17	chr1:179099200-179114800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr1:179099400-179106800	Weak transcription	Pancreas	Pancrea
19	chr1:179099400-179106800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr1:179099400-179106800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr1:179099400-179107000	Weak transcription	Placenta	Placenta
22	chr1:179099400-179110000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:179099400-179110400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr1:179099400-179112000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:179099400-179112000	Weak transcription	Left Ventricle	heart
26	chr1:179099600-179106800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:179099600-179106800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr1:179099600-179109200	Weak transcription	Primary T cells from cord blood	blood
29	chr1:179099600-179109800	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr1:179099600-179109800	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr1:179099600-179110000	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr1:179099600-179110200	Weak transcription	Primary B cells from peripheral blood	blood
33	chr1:179099600-179110600	Weak transcription	Rectal Smooth Muscle	rectum
34	chr1:179099600-179110800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr1:179099600-179116800	Weak transcription	Thymus	Thymus
36	chr1:179099600-179119400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:179099600-179122600	Weak transcription	Stomach Smooth Muscle	stomach
38	chr1:179099800-179106400	Weak transcription	Hela-S3	cervix
39	chr1:179099800-179107000	Weak transcription	Adipose Nuclei	Adipose
40	chr1:179099800-179107000	Weak transcription	Psoas Muscle	Psoas
41	chr1:179099800-179108800	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr1:179099800-179109400	Weak transcription	Primary B cells from cord blood	blood
43	chr1:179099800-179111800	Weak transcription	HepG2	liver
44	chr1:179100000-179105200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr1:179100000-179106000	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr1:179100000-179108600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr1:179100000-179121000	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr1:179100200-179110000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr1:179100600-179106000	Weak transcription	Liver	Liver
50	chr1:179100600-179110800	Weak transcription	Brain Inferior Temporal Lobe	brain

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