Variant report

Variant	rs59432349
Chromosome Location	chr15:56465444-56465445
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:56464843..56467982-chr15:56534893..56537974,3	K562	blood:

Variant related genes	Relation type
ENSG00000181827	Chromatin interaction
ENSG00000151575	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs11629483	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11631191	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12905899	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12907263	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12911094	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12911427	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12914260	0.82[EUR][1000 genomes]
rs12914640	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1372753	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1442640	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1829542	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2119937	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2414464	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2460647	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2460648	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2460650	0.86[EUR][1000 genomes]
rs2682044	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2682046	0.92[ASN][1000 genomes]
rs2682049	0.86[EUR][1000 genomes]
rs2682051	0.87[EUR][1000 genomes]
rs2682053	0.87[EUR][1000 genomes]
rs2682054	0.87[EUR][1000 genomes]
rs2713923	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2713924	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2713926	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2713933	0.87[EUR][1000 genomes]
rs2713936	0.86[EUR][1000 genomes]
rs2713938	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2713941	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2718915	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2718941	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2725870	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34044869	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34144128	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34224072	0.87[EUR][1000 genomes]
rs34386737	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34756325	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35082998	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35722267	0.82[EUR][1000 genomes]
rs35749329	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35972806	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4310791	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4310792	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4774231	0.86[EUR][1000 genomes]
rs4774232	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4774847	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4774848	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62044082	0.83[EUR][1000 genomes]
rs62044110	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62044111	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6493835	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7165270	0.87[EUR][1000 genomes]
rs7168319	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7174823	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7175745	0.87[EUR][1000 genomes]
rs7496025	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8024031	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8028353	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8029114	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8032242	0.85[EUR][1000 genomes]
rs8033653	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9672886	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9672928	0.94[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs59432349	RFX7	cis	Adipose Subcutaneous	GTEx
rs59432349	RFX7	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56442600-56470600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr15:56446600-56468400	Weak transcription	Fetal Lung	lung
3	chr15:56453000-56479600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr15:56453600-56515000	Weak transcription	NHLF	lung
5	chr15:56454400-56465600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr15:56454400-56466400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr15:56454400-56467000	Weak transcription	Brain Angular Gyrus	brain
8	chr15:56454400-56467200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr15:56454400-56470000	Weak transcription	Colon Smooth Muscle	Colon
10	chr15:56454400-56470200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr15:56454400-56473400	Weak transcription	K562	blood
12	chr15:56454600-56465600	Weak transcription	Brain Substantia Nigra	brain
13	chr15:56454600-56484000	Weak transcription	Brain Anterior Caudate	brain
14	chr15:56456600-56484800	Weak transcription	Aorta	Aorta
15	chr15:56457200-56469000	Weak transcription	Hela-S3	cervix
16	chr15:56457400-56500400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr15:56457800-56471600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr15:56458000-56470200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr15:56458000-56474000	Weak transcription	Pancreas	Pancrea
20	chr15:56458200-56465800	Weak transcription	Lung	lung
21	chr15:56458400-56496200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr15:56459200-56466600	Weak transcription	HUVEC	blood vessel
23	chr15:56459200-56469400	Weak transcription	Psoas Muscle	Psoas
24	chr15:56459200-56511000	Weak transcription	Esophagus	oesophagus
25	chr15:56459400-56484400	Weak transcription	Spleen	Spleen
26	chr15:56459600-56473200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr15:56460200-56480800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr15:56460600-56467000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr15:56460800-56467600	Weak transcription	Brain Hippocampus Middle	brain
30	chr15:56461000-56466600	Weak transcription	Left Ventricle	heart
31	chr15:56461000-56466800	Weak transcription	Adipose Nuclei	Adipose
32	chr15:56461000-56467000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr15:56461000-56470200	Strong transcription	Dnd41	blood
34	chr15:56461000-56470600	Weak transcription	NHDF-Ad	bronchial
35	chr15:56461200-56469200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr15:56461200-56469400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr15:56461400-56465800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr15:56461400-56466800	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr15:56461400-56482400	Weak transcription	Ovary	ovary
40	chr15:56461600-56470600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr15:56462000-56465600	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr15:56462000-56466200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr15:56462200-56466000	Strong transcription	Primary B cells from cord blood	blood
44	chr15:56462200-56466000	Strong transcription	Primary B cells from peripheral blood	blood
45	chr15:56462200-56466000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr15:56462200-56466200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr15:56462400-56466400	Strong transcription	Fetal Thymus	thymus
48	chr15:56462400-56467200	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr15:56462600-56465800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr15:56462600-56466000	Strong transcription	Duodenum Mucosa	Duodenum

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