Variant report

Variant	rs62044111
Chromosome Location	chr15:56442425-56442426
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs11629483	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631191	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12905899	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12907263	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12911094	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12911427	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12914260	0.89[EUR][1000 genomes]
rs12914640	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1372753	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1442640	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1829542	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2119937	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2414464	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2460647	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2460648	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2682044	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2682046	0.88[ASN][1000 genomes]
rs2682051	0.81[EUR][1000 genomes]
rs2682053	0.80[EUR][1000 genomes]
rs2682054	0.80[EUR][1000 genomes]
rs2713923	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2713924	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2713926	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2713933	0.80[EUR][1000 genomes]
rs2713938	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2713941	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2718915	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2718941	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2725870	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34044869	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34144128	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34224072	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34386737	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34756325	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs35082998	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35722267	0.88[EUR][1000 genomes]
rs35749329	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35972806	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4310791	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4310792	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4774231	0.93[EUR][1000 genomes]
rs4774232	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4774847	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4774848	0.83[ASN][1000 genomes]
rs59432349	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62044082	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62044110	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493835	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7165270	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7168319	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7174823	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7175745	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7496025	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8024031	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8028353	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8029114	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8032242	0.91[EUR][1000 genomes]
rs8033653	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9672886	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9672928	0.87[EUR][1000 genomes];0.93[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	nsv833018	chr15:56325799-56492535	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1045906	chr15:56333180-56473614	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62044111	RFX7	cis	lung	GTEx
rs62044111	RFX7	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56424800-56453800	Weak transcription	Brain Substantia Nigra	brain
2	chr15:56429400-56442600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr15:56431600-56442800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:56433800-56464000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr15:56435200-56442600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr15:56435200-56458800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr15:56435400-56442600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr15:56435400-56443000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr15:56435400-56443400	Weak transcription	Placenta	Placenta
10	chr15:56435400-56444200	Weak transcription	Brain Anterior Caudate	brain
11	chr15:56435400-56444600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr15:56435400-56444600	Weak transcription	Brain Angular Gyrus	brain
13	chr15:56435400-56446800	Weak transcription	Primary B cells from peripheral blood	blood
14	chr15:56435400-56447200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr15:56435400-56461000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr15:56435400-56462400	Weak transcription	Fetal Thymus	thymus
17	chr15:56435400-56465200	Weak transcription	Thymus	Thymus
18	chr15:56435800-56444200	Weak transcription	Fetal Intestine Large	intestine
19	chr15:56435800-56454000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr15:56436000-56448600	Weak transcription	K562	blood
21	chr15:56436000-56458000	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr15:56436400-56455800	Weak transcription	Liver	Liver
23	chr15:56436600-56442600	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr15:56436600-56443600	Weak transcription	Dnd41	blood
25	chr15:56436600-56458800	Weak transcription	Primary B cells from cord blood	blood
26	chr15:56438000-56442600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr15:56438200-56443600	Weak transcription	Osteobl	bone
28	chr15:56438600-56444200	Weak transcription	Left Ventricle	heart
29	chr15:56439000-56443200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr15:56439400-56442800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr15:56440200-56443000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr15:56440400-56443000	Strong transcription	Primary T cells from cord blood	blood
33	chr15:56440600-56443400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
34	chr15:56440800-56442800	Weak transcription	Duodenum Mucosa	Duodenum
35	chr15:56440800-56445400	Weak transcription	Fetal Muscle Trunk	muscle
36	chr15:56441000-56444600	Weak transcription	Fetal Lung	lung
37	chr15:56441000-56453200	Weak transcription	A549	lung
38	chr15:56441000-56461400	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr15:56441200-56443000	ZNF genes & repeats	Fetal Intestine Small	intestine
40	chr15:56441400-56445200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr15:56441600-56442600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr15:56441600-56442600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr15:56441600-56442800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr15:56441600-56443000	Enhancers	Spleen	Spleen
45	chr15:56441800-56442800	ZNF genes & repeats	Fetal Stomach	stomach
46	chr15:56442000-56442600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr15:56442000-56442600	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr15:56442000-56443000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr15:56442000-56457200	Weak transcription	HMEC	breast
50	chr15:56442000-56458000	Weak transcription	HepG2	liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links