Variant report

Variant	rs7496025
Chromosome Location	chr15:56436357-56436358
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs11629483	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11631191	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12905899	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12907263	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12911094	0.82[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12911427	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12914260	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12914640	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1372753	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]
rs1442640	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1829542	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2119937	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2249090	0.92[CEU][hapmap]
rs2414464	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2460647	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2460648	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2460650	1.00[CEU][hapmap]
rs2682044	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2682046	0.93[ASN][1000 genomes]
rs2682051	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2682053	0.80[AMR][1000 genomes]
rs2682054	1.00[CEU][hapmap]
rs2682059	1.00[CEU][hapmap]
rs2713923	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2713924	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2713926	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2713933	1.00[CEU][hapmap];0.83[CHB][hapmap];0.80[AMR][1000 genomes]
rs2713935	0.81[CEU][hapmap];0.83[CHB][hapmap]
rs2713936	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs2713938	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2713941	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2718915	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2718921	0.88[YRI][hapmap]
rs2718934	1.00[CEU][hapmap]
rs2718941	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2725854	0.96[CEU][hapmap];0.83[CHB][hapmap];0.94[LWK][hapmap];0.96[MKK][hapmap];0.88[YRI][hapmap]
rs2725870	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2947021	0.92[CEU][hapmap]
rs34044869	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34144128	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34224072	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34386737	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34756325	0.87[ASN][1000 genomes]
rs35082998	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35722267	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35749329	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35972806	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4310791	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4310792	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4774231	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4774232	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4774847	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4774848	0.85[ASN][1000 genomes]
rs59432349	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62044082	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62044110	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62044111	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6493835	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7165270	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7168319	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7174823	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7175745	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7176107	0.80[CEU][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap]
rs8024031	0.82[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8028353	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8029114	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8032242	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8033653	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9672886	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9672928	1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7496025	RFX7	cis	Adipose Subcutaneous	GTEx
rs7496025	RFXDC2	cis	multi-tissue	Pritchard
rs7496025	FLJ12994	cis	multi-tissue	Pritchard
rs7496025	RFX7	cis	Skin Sun Exposed Lower leg	GTEx
rs7496025	RFX7	cis	lymphoblastoid	seeQTL
rs7496025	RFX7	cis	lung	GTEx

Chromatin state (count:114 , 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	chr15:56416200-56437800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr15:56416200-56441600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr15:56419200-56438400	Weak transcription	Psoas Muscle	Psoas
8	chr15:56419600-56439000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr15:56421600-56437800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr15:56422200-56440400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr15:56424800-56453800	Weak transcription	Brain Substantia Nigra	brain
12	chr15:56427000-56439600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr15:56429200-56437200	Weak transcription	Colon Smooth Muscle	Colon
14	chr15:56429400-56442600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr15:56429600-56437800	Weak transcription	Small Intestine	intestine
16	chr15:56429600-56441200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr15:56431600-56442800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr15:56431800-56437800	Weak transcription	Ovary	ovary
19	chr15:56432000-56438000	Weak transcription	Right Ventricle	heart
20	chr15:56432400-56436600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr15:56432400-56437800	Weak transcription	Fetal Heart	heart
22	chr15:56432600-56436400	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr15:56432800-56436600	Strong transcription	Primary B cells from cord blood	blood
24	chr15:56433000-56436400	Strong transcription	Liver	Liver
25	chr15:56433000-56436600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr15:56433000-56436600	Strong transcription	NHEK	skin
27	chr15:56433600-56436600	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr15:56433600-56436600	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr15:56433600-56436800	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr15:56433600-56437000	Weak transcription	Aorta	Aorta
31	chr15:56433600-56438400	Weak transcription	Fetal Intestine Small	intestine
32	chr15:56433800-56436400	Weak transcription	Fetal Brain Male	brain
33	chr15:56433800-56436600	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr15:56433800-56436600	Strong transcription	Dnd41	blood
35	chr15:56433800-56437800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr15:56433800-56464000	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr15:56434600-56436600	Strong transcription	HepG2	liver
38	chr15:56435200-56436400	Weak transcription	NHLF	lung
39	chr15:56435200-56436800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr15:56435200-56436800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr15:56435200-56436800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr15:56435200-56437000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr15:56435200-56437000	Weak transcription	Brain Hippocampus Middle	brain
44	chr15:56435200-56437000	Weak transcription	NHDF-Ad	bronchial
45	chr15:56435200-56437400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr15:56435200-56437600	Weak transcription	Fetal Brain Female	brain
47	chr15:56435200-56437800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr15:56435200-56440000	Weak transcription	Fetal Muscle Trunk	muscle
49	chr15:56435200-56440600	Weak transcription	Fetal Lung	lung
50	chr15:56435200-56441800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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