Variant report

Variant	rs2713938
Chromosome Location	chr15:56495879-56495880
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:56492206..56494642-chr15:56495488..56498069,2	MCF-7	breast:
2	chr15:56494171..56496972-chr15:56541763..56543619,2	K562	blood:
3	chr15:56495337..56498069-chr15:56534935..56537509,2	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:62)

rs_ID	r²[population]
rs11629483	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11631191	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12905899	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12907263	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12911094	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12911427	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12914640	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1372753	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1442640	0.83[EUR][1000 genomes]
rs1829542	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2119937	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2414464	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2460647	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2460648	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2460650	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2682019	0.82[AFR][1000 genomes]
rs2682044	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682046	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2682049	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2682051	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2682053	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2682054	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2713923	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2713924	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2713926	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2713931	0.82[AFR][1000 genomes]
rs2713933	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2713936	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2713941	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2718915	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2718941	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2725870	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34044869	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34144128	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34224072	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34386737	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34756325	0.88[ASN][1000 genomes]
rs35082998	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35749329	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35972806	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4310791	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4310792	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4774231	0.81[EUR][1000 genomes]
rs4774232	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4774847	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4774848	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59432349	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62044082	0.81[ASN][1000 genomes]
rs62044110	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62044111	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6493835	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7165270	0.82[EUR][1000 genomes]
rs7168319	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7174823	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7175745	0.82[EUR][1000 genomes]
rs7496025	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8024031	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8028353	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8029114	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8033653	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9672886	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9672928	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[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	nsv519725	chr15:56485598-56496582	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv833019	chr15:56486029-56649933	Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv528965	chr15:56489159-56504598	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2713938	RFX7	cis	Adipose Subcutaneous	GTEx
rs2713938	RFX7	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56453600-56515000	Weak transcription	NHLF	lung
2	chr15:56457400-56500400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:56458400-56496200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:56459200-56511000	Weak transcription	Esophagus	oesophagus
5	chr15:56463600-56496600	Weak transcription	NHEK	skin
6	chr15:56464600-56497800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:56465400-56496600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr15:56465800-56496000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr15:56465800-56496600	Weak transcription	HMEC	breast
10	chr15:56466000-56497000	Weak transcription	HSMMtube	muscle
11	chr15:56466000-56500000	Weak transcription	Thymus	Thymus
12	chr15:56466000-56514200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr15:56467000-56500400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr15:56467000-56511600	Weak transcription	Fetal Intestine Small	intestine
15	chr15:56470200-56498800	Weak transcription	Dnd41	blood
16	chr15:56470800-56496400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr15:56470800-56503800	Weak transcription	Fetal Lung	lung
18	chr15:56476600-56496200	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr15:56477000-56500400	Weak transcription	Liver	Liver
20	chr15:56477200-56497000	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr15:56479800-56496200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr15:56480000-56496200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr15:56480000-56496600	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr15:56480000-56500000	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr15:56480200-56497000	Weak transcription	HUVEC	blood vessel
26	chr15:56480200-56515400	Weak transcription	Hela-S3	cervix
27	chr15:56480800-56496200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr15:56481400-56497800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr15:56482600-56497000	Weak transcription	NH-A	brain
30	chr15:56482600-56500200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr15:56484800-56496200	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr15:56484800-56500000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr15:56485000-56502800	Weak transcription	Gastric	stomach
34	chr15:56485600-56500000	Weak transcription	Aorta	Aorta
35	chr15:56485600-56521200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr15:56486600-56497000	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr15:56486800-56496600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr15:56488200-56497000	Weak transcription	HSMM	muscle
39	chr15:56488400-56496800	Weak transcription	Fetal Brain Male	brain
40	chr15:56489200-56497200	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr15:56489200-56503600	Weak transcription	Primary hematopoietic stem cells	blood
42	chr15:56490600-56497400	Weak transcription	HepG2	liver
43	chr15:56490800-56497000	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr15:56491600-56497000	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr15:56491600-56497400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr15:56491800-56496400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr15:56492000-56496800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr15:56492200-56497200	Weak transcription	A549	lung
49	chr15:56492400-56497400	Weak transcription	Primary T cells from cord blood	blood
50	chr15:56493000-56500000	Weak transcription	Ovary	ovary

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