Variant report

Variant	rs790055
Chromosome Location	chr1:160971146-160971147
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:160970390-160971572	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:160970990..160972886-chr1:160988444..160990539,2	MCF-7	breast:
2	chr1:160969057..160971514-chr1:161037864..161040165,2	K562	blood:

Variant related genes	Relation type
F11R	TF binding region
ENSG00000186517	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10737178	0.83[CHB][hapmap];0.86[CHD][hapmap]
rs10908820	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12132502	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12758348	0.86[ASN][1000 genomes]
rs2039223	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2184065	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs2246145	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2246485	0.91[CEU][hapmap]
rs2247472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2249933	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2250174	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2250193	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2250304	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2256625	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs2481076	0.96[ASN][1000 genomes]
rs2481077	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2483139	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs2483141	0.92[CEU][hapmap];0.92[CHB][hapmap];0.87[YRI][hapmap]
rs2483142	0.80[EUR][1000 genomes]
rs2990706	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3007155	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4396136	0.81[MEX][hapmap]
rs4483427	0.81[ASN][1000 genomes]
rs6427571	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6677526	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7512280	0.82[ASN][1000 genomes]
rs7542911	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs790056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv548058	chr1:160925455-160989614	Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs790055	OR6K3	cis	cerebellum	SCAN
rs790055	F11R	cis	cerebellum	SCAN
rs790055	TSTD1	cis	Artery Tibial	GTEx
rs790055	NHLH1	cis	parietal	SCAN
rs790055	TSTD1	cis	Adipose Subcutaneous	GTEx
rs790055	F11R	cis	lymphoblastoid	seeQTL
rs790055	F11R	cis	parietal	SCAN
rs790055	F11R	Cis_1M	lymphoblastoid	RTeQTL
rs790055	PAQR6	cis	cerebellum	SCAN
rs790055	OR10R2	cis	parietal	SCAN
rs790055	RXFP4	cis	parietal	SCAN
rs790055	TSTD1	cis	Nerve Tibial	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160960400-160978400	Weak transcription	Fetal Lung	lung
2	chr1:160960600-160977400	Weak transcription	Fetal Kidney	kidney
3	chr1:160960600-160981600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr1:160963400-160983000	Weak transcription	HSMMtube	muscle
5	chr1:160964400-160972600	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr1:160965000-160971800	Strong transcription	H1 Cell Line	embryonic stem cell
7	chr1:160965400-160972600	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr1:160966600-160971800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:160966600-160971800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr1:160966800-160971200	Strong transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:160966800-160972600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:160967000-160971200	Strong transcription	Fetal Thymus	thymus
13	chr1:160967000-160971600	Strong transcription	Esophagus	oesophagus
14	chr1:160967000-160971800	Strong transcription	H9 Cell Line	embryonic stem cell
15	chr1:160967000-160971800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
16	chr1:160967000-160972400	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr1:160967400-160971200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:160967400-160972400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:160967600-160971400	Strong transcription	Primary B cells from cord blood	blood
20	chr1:160967600-160971400	Strong transcription	Primary hematopoietic stem cells	blood
21	chr1:160967600-160971600	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr1:160967600-160971800	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr1:160967600-160971800	Strong transcription	Fetal Stomach	stomach
24	chr1:160967600-160971800	Strong transcription	NHEK	skin
25	chr1:160967600-160972200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr1:160967600-160972200	Strong transcription	Primary T cells from cord blood	blood
27	chr1:160967600-160972600	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr1:160967800-160971200	Strong transcription	Adipose Nuclei	Adipose
29	chr1:160967800-160971200	Strong transcription	Stomach Smooth Muscle	stomach
30	chr1:160967800-160971400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr1:160967800-160971400	Weak transcription	Brain Substantia Nigra	brain
32	chr1:160967800-160971600	Weak transcription	Brain Anterior Caudate	brain
33	chr1:160967800-160971800	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr1:160967800-160971800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:160967800-160971800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr1:160967800-160971800	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr1:160967800-160971800	Strong transcription	HMEC	breast
38	chr1:160967800-160978200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr1:160967800-160978800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr1:160968000-160971200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr1:160968000-160971200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr1:160968000-160971200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr1:160968000-160971200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:160968000-160971200	Strong transcription	Pancreas	Pancrea
45	chr1:160968000-160971200	Strong transcription	Spleen	Spleen
46	chr1:160968000-160971400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr1:160968000-160971600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr1:160968000-160971800	Strong transcription	HepG2	liver
49	chr1:160968000-160972200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr1:160968000-160976800	Weak transcription	Brain Angular Gyrus	brain

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