Variant report

Variant	rs2792561
Chromosome Location	chr1:213038375-213038376
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:213032682..213037696-chr1:213038069..213043473,6	K562	blood:
2	chr1:213031674..213033675-chr1:213035938..213038632,2	MCF-7	breast:
3	chr1:213032255..213037228-chr1:213037322..213040248,4	K562	blood:

Variant related genes	Relation type
ENSG00000162769	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10127459	1.00[ASN][1000 genomes]
rs10746436	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10779594	1.00[CHB][hapmap];0.81[GIH][hapmap];0.86[MEX][hapmap];1.00[ASN][1000 genomes]
rs10864003	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10864019	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11120033	1.00[ASN][1000 genomes]
rs11804466	1.00[CHB][hapmap]
rs11808834	1.00[CHB][hapmap]
rs11810592	1.00[CHB][hapmap]
rs12036735	1.00[ASN][1000 genomes]
rs1284800	1.00[ASN][1000 genomes]
rs1284864	1.00[ASN][1000 genomes]
rs1615680	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1692178	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1692179	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1692180	1.00[ASN][1000 genomes]
rs17020044	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17020046	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1770777	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1770778	1.00[ASN][1000 genomes]
rs1874419	1.00[ASN][1000 genomes]
rs2047289	1.00[ASN][1000 genomes]
rs2047293	1.00[ASN][1000 genomes]
rs2359321	1.00[CHB][hapmap]
rs2359324	1.00[ASN][1000 genomes]
rs2456815	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2644545	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2792558	1.00[ASN][1000 genomes]
rs2792560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35976699	1.00[ASN][1000 genomes]
rs41315581	1.00[ASN][1000 genomes]
rs4951467	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4951649	1.00[CHB][hapmap];0.81[GIH][hapmap];0.86[MEX][hapmap];1.00[ASN][1000 genomes]
rs59252582	1.00[ASN][1000 genomes]
rs6540768	1.00[ASN][1000 genomes]
rs6666362	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6667161	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6674933	1.00[CHB][hapmap];0.81[GIH][hapmap];0.86[MEX][hapmap];1.00[ASN][1000 genomes]
rs6689134	1.00[ASN][1000 genomes]
rs6703612	1.00[ASN][1000 genomes]
rs7518378	1.00[CHB][hapmap]
rs7528119	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[ASN][1000 genomes]
rs7533932	1.00[ASN][1000 genomes]
rs7542906	1.00[ASN][1000 genomes]
rs963327	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011186	chr1:213005165-213069563	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1013705	chr1:213005344-213064209	Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1008383	chr1:213025546-213114894	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv998261	chr1:213029814-213064209	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv998979	chr1:213029814-213073013	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv1007129	chr1:213037244-213083261	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2792561	FLVCR1	cis	cerebellum	SCAN
rs2792561	FAM71A	cis	cerebellum	SCAN
rs2792561	LQK1	Cis_1M	lymphoblastoid	RTeQTL
rs2792561	FLVCR1-AS1	cis	Artery Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213032600-213046400	Weak transcription	Ovary	ovary
2	chr1:213032600-213049200	Weak transcription	Right Atrium	heart
3	chr1:213032600-213073000	Weak transcription	Colonic Mucosa	Colon
4	chr1:213032600-213073000	Weak transcription	Esophagus	oesophagus
5	chr1:213032800-213046400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr1:213032800-213048000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr1:213032800-213056800	Weak transcription	Fetal Thymus	thymus
8	chr1:213032800-213057800	Weak transcription	Placenta	Placenta
9	chr1:213032800-213061800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:213032800-213062000	Weak transcription	Psoas Muscle	Psoas
11	chr1:213033400-213046800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr1:213033400-213046800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr1:213033600-213046800	Weak transcription	Liver	Liver
14	chr1:213033600-213048600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr1:213033600-213062000	Weak transcription	Thymus	Thymus
16	chr1:213034400-213041200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:213034400-213044800	Weak transcription	HSMMtube	muscle
18	chr1:213034400-213046200	Weak transcription	Fetal Lung	lung
19	chr1:213034400-213046600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr1:213034400-213046600	Weak transcription	Brain Cingulate Gyrus	brain
21	chr1:213034400-213048200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr1:213034400-213048400	Weak transcription	Brain Hippocampus Middle	brain
23	chr1:213034400-213058000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr1:213034400-213068000	Weak transcription	Colon Smooth Muscle	Colon
25	chr1:213034600-213039000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:213034600-213039600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr1:213034600-213041400	Weak transcription	Fetal Stomach	stomach
28	chr1:213034600-213044200	Weak transcription	Aorta	Aorta
29	chr1:213034600-213044800	Weak transcription	Left Ventricle	heart
30	chr1:213034600-213044800	Weak transcription	Pancreas	Pancrea
31	chr1:213034600-213046000	Weak transcription	HMEC	breast
32	chr1:213034600-213046400	Weak transcription	Brain Anterior Caudate	brain
33	chr1:213034600-213046400	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr1:213034600-213046600	Weak transcription	Primary B cells from peripheral blood	blood
35	chr1:213034600-213046800	Weak transcription	Primary B cells from cord blood	blood
36	chr1:213034600-213046800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:213034600-213046800	Weak transcription	NHDF-Ad	bronchial
38	chr1:213034600-213047400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr1:213034600-213048000	Weak transcription	Spleen	Spleen
40	chr1:213034600-213048600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr1:213034600-213048600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr1:213034600-213049200	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr1:213034600-213049200	Weak transcription	Lung	lung
44	chr1:213034600-213049400	Weak transcription	Gastric	stomach
45	chr1:213034600-213056200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr1:213034600-213057000	Weak transcription	Brain Substantia Nigra	brain
47	chr1:213034600-213057000	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr1:213034600-213057200	Weak transcription	Right Ventricle	heart
49	chr1:213034600-213061800	Weak transcription	Fetal Heart	heart
50	chr1:213034600-213067800	Weak transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links