Variant report

Variant	rs1372753
Chromosome Location	chr15:56433240-56433241
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs11629483	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11631191	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12905899	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12907263	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12911094	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12911427	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12914260	0.80[EUR][1000 genomes]
rs12914640	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1442640	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1829542	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2119937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2249090	0.85[CEU][hapmap];0.86[MEX][hapmap]
rs2414464	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2460647	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2460648	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2460650	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2682044	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2682046	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2682049	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2682051	0.92[CEU][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2682053	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2682054	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2682059	0.92[CEU][hapmap]
rs2713923	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2713924	0.92[CEU][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2713926	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2713933	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2713935	0.87[CHB][hapmap]
rs2713936	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2713938	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2713941	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2718915	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2718934	0.92[CEU][hapmap]
rs2718941	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2725854	0.96[CEU][hapmap]
rs2725870	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2947021	0.85[CEU][hapmap]
rs34044869	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34144128	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34224072	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34386737	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34756325	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35082998	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35722267	0.87[EUR][1000 genomes]
rs35749329	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35972806	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4310791	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4310792	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4774231	0.84[EUR][1000 genomes]
rs4774232	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4774847	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4774848	0.81[ASN][1000 genomes]
rs59432349	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62044082	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62044110	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62044111	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6493835	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7165270	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7168319	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7174823	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7175745	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7176107	0.88[CEU][hapmap];0.88[TSI][hapmap]
rs7496025	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8024031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8028353	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8029114	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8032242	0.83[EUR][1000 genomes]
rs8033653	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9672886	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9672928	0.82[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[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
rs1372753	RFX7	cis	Skin Sun Exposed Lower leg	GTEx
rs1372753	RFX7	cis	lymphoblastoid	seeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56388800-56437200	Weak transcription	Pancreas	Pancrea
2	chr15:56388800-56441600	Weak transcription	Lung	lung
3	chr15:56411600-56436800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr15:56413400-56441600	Weak transcription	Spleen	Spleen
5	chr15:56416200-56434800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr15:56416200-56437800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr15:56416200-56441600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:56416400-56434600	Weak transcription	NH-A	brain
9	chr15:56419200-56434200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr15:56419200-56438400	Weak transcription	Psoas Muscle	Psoas
11	chr15:56419400-56434000	Weak transcription	HMEC	breast
12	chr15:56419600-56434400	Weak transcription	NHDF-Ad	bronchial
13	chr15:56419600-56439000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr15:56420400-56434000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr15:56420400-56434800	Weak transcription	HSMMtube	muscle
16	chr15:56421000-56433400	Weak transcription	Brain Angular Gyrus	brain
17	chr15:56421600-56437800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr15:56422200-56434800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr15:56422200-56440400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr15:56423400-56433400	Weak transcription	HepG2	liver
21	chr15:56423800-56434600	Weak transcription	Left Ventricle	heart
22	chr15:56424800-56453800	Weak transcription	Brain Substantia Nigra	brain
23	chr15:56427000-56439600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr15:56427200-56434800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr15:56429200-56437200	Weak transcription	Colon Smooth Muscle	Colon
26	chr15:56429400-56442600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr15:56429600-56437800	Weak transcription	Small Intestine	intestine
28	chr15:56429600-56441200	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr15:56431600-56433600	Strong transcription	Fetal Stomach	stomach
30	chr15:56431600-56433800	Weak transcription	HUVEC	blood vessel
31	chr15:56431600-56434800	Weak transcription	NHLF	lung
32	chr15:56431600-56442800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr15:56431800-56434000	Weak transcription	Placenta	Placenta
34	chr15:56431800-56436000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr15:56431800-56437800	Weak transcription	Ovary	ovary
36	chr15:56432000-56434800	Weak transcription	Brain Anterior Caudate	brain
37	chr15:56432000-56438000	Weak transcription	Right Ventricle	heart
38	chr15:56432400-56436600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr15:56432400-56437800	Weak transcription	Fetal Heart	heart
40	chr15:56432600-56433600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr15:56432600-56433800	ZNF genes & repeats	Dnd41	blood
42	chr15:56432600-56435200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr15:56432600-56435400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr15:56432600-56435400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr15:56432600-56435400	Strong transcription	Duodenum Mucosa	Duodenum
46	chr15:56432600-56435800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr15:56432600-56436200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:56432600-56436400	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr15:56432800-56433600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
50	chr15:56432800-56433600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell

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