Variant report

Variant	rs34144128
Chromosome Location	chr15:56413338-56413339
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11629483	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11631191	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12905899	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12907263	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12911094	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12911427	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12914260	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12914640	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1372753	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1442640	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1829542	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2119937	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2414464	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2460647	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2460648	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2682044	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2682046	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2682051	0.82[AMR][1000 genomes]
rs2682053	0.80[AMR][1000 genomes]
rs2713923	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2713924	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2713926	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2713933	0.80[AMR][1000 genomes]
rs2713936	0.81[AMR][1000 genomes]
rs2713938	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2713941	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2718915	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2718941	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2725870	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34044869	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34224072	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34386737	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34756325	0.92[ASN][1000 genomes]
rs35082998	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35722267	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35749329	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35972806	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4310791	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4310792	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4774231	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4774232	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4774847	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59432349	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62044082	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62044110	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62044111	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6493835	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7165270	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7168319	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7174823	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7175745	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7496025	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8024031	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8028353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8029114	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8032242	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8033653	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9672886	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9672928	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761872	chr15:56211065-56426501	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	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
3	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs34144128	RFX7	cis	Adipose Subcutaneous	GTEx
rs34144128	RFX7	cis	lung	GTEx
rs34144128	RFX7	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56388800-56414400	Weak transcription	Thymus	Thymus
2	chr15:56388800-56418400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr15:56388800-56433000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr15:56388800-56437200	Weak transcription	Pancreas	Pancrea
5	chr15:56388800-56441600	Weak transcription	Lung	lung
6	chr15:56389400-56418400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr15:56389400-56418400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr15:56389600-56414400	Weak transcription	HSMMtube	muscle
9	chr15:56389800-56415600	Weak transcription	Placenta	Placenta
10	chr15:56390400-56414400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr15:56390600-56414200	Weak transcription	Fetal Lung	lung
12	chr15:56390600-56414200	Weak transcription	Left Ventricle	heart
13	chr15:56390600-56414600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr15:56390600-56416400	Weak transcription	HUVEC	blood vessel
15	chr15:56390600-56417400	Weak transcription	Adipose Nuclei	Adipose
16	chr15:56390600-56418000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr15:56390800-56418600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr15:56391800-56415800	Weak transcription	Ovary	ovary
19	chr15:56392600-56417200	Weak transcription	Brain Hippocampus Middle	brain
20	chr15:56394000-56414200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr15:56394000-56418200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr15:56394200-56417000	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr15:56394400-56414000	Weak transcription	HMEC	breast
24	chr15:56394400-56414200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr15:56394400-56414200	Weak transcription	NH-A	brain
26	chr15:56394800-56414800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr15:56395000-56415800	Weak transcription	Fetal Thymus	thymus
28	chr15:56395000-56418200	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr15:56395200-56414200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr15:56397000-56414200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr15:56397200-56414200	Weak transcription	Primary T cells from cord blood	blood
32	chr15:56405400-56414200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr15:56405800-56414800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr15:56407600-56414200	Weak transcription	HSMM	muscle
35	chr15:56407800-56414200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr15:56408000-56418200	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr15:56408400-56414400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr15:56408600-56414200	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr15:56409400-56418400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr15:56410200-56413400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr15:56410800-56419400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr15:56411400-56414400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr15:56411400-56424000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr15:56411600-56436800	Weak transcription	Stomach Smooth Muscle	stomach
45	chr15:56411800-56414600	Weak transcription	Fetal Kidney	kidney
46	chr15:56411800-56418600	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr15:56411800-56419600	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr15:56412000-56414200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr15:56412000-56414600	Weak transcription	Fetal Stomach	stomach
50	chr15:56412000-56418200	Weak transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links