Variant report

Variant	rs2718941
Chromosome Location	chr15:56522181-56522182
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:56521792..56524721-chr15:56527729..56529667,2	MCF-7	breast:
2	chr15:56517945..56522475-chr15:56532942..56536961,5	K562	blood:

Variant related genes	Relation type
ENSG00000181827	Chromatin interaction
ENSG00000151575	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs11629483	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11631191	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12900678	0.96[CEU][hapmap];0.88[YRI][hapmap]
rs12905782	0.92[CEU][hapmap]
rs12905899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12911094	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12911427	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12914640	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1372753	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]
rs1549452	1.00[CEU][hapmap]
rs17819438	1.00[CEU][hapmap]
rs1829542	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2119937	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2249090	0.92[CEU][hapmap]
rs2303441	1.00[CEU][hapmap];0.89[YRI][hapmap]
rs2414464	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2460647	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2460648	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2460650	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2682044	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2682046	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2682049	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2682051	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2682053	0.80[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2682054	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2682059	0.96[CEU][hapmap]
rs2713923	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2713924	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2713926	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2713933	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2713935	0.82[CEU][hapmap];0.88[CHB][hapmap];0.80[JPT][hapmap]
rs2713936	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2713938	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2713941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2718915	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2718921	0.89[YRI][hapmap]
rs2718934	1.00[CEU][hapmap]
rs2725854	0.96[CEU][hapmap];0.88[YRI][hapmap]
rs2725870	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2947021	0.92[CEU][hapmap]
rs34044869	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs34144128	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34224072	0.84[AMR][1000 genomes]
rs34386737	0.88[ASN][1000 genomes]
rs34756325	0.84[ASN][1000 genomes]
rs35082998	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35749329	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35972806	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3817406	0.96[CEU][hapmap];0.89[YRI][hapmap]
rs4310791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4310792	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4774232	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4774847	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4774848	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59432349	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62044110	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62044111	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6493835	0.84[ASN][1000 genomes]
rs6493856	0.96[CEU][hapmap]
rs7168319	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7174823	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7176107	0.80[CEU][hapmap]
rs7496025	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]
rs8024031	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8028353	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8029114	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8033653	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9672886	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9672928	0.83[CHB][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[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	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
2	nsv569547	chr15:56504598-56572176	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	esv2760380	chr15:56510123-56529955	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2718941	RFX7	cis	Skin Sun Exposed Lower leg	GTEx
rs2718941	RFX7	cis	Adipose Subcutaneous	GTEx
rs2718941	FLJ12994	cis	multi-tissue	Pritchard

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56508000-56534400	Weak transcription	Fetal Heart	heart
2	chr15:56508200-56524000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr15:56508400-56523000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr15:56509000-56533600	Weak transcription	Osteobl	bone
5	chr15:56509800-56522400	Weak transcription	Fetal Brain Male	brain
6	chr15:56510200-56523200	Weak transcription	NH-A	brain
7	chr15:56510600-56528600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr15:56513800-56523800	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr15:56513800-56530200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
10	chr15:56514000-56535000	Weak transcription	Pancreas	Pancrea
11	chr15:56514600-56532400	Weak transcription	HSMMtube	muscle
12	chr15:56514800-56534800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr15:56515400-56522800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr15:56515400-56523600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr15:56515600-56522400	Weak transcription	HMEC	breast
16	chr15:56515600-56522800	Weak transcription	Fetal Thymus	thymus
17	chr15:56515600-56523000	Weak transcription	Thymus	Thymus
18	chr15:56515600-56524000	Weak transcription	Aorta	Aorta
19	chr15:56515600-56524000	Weak transcription	Ovary	ovary
20	chr15:56515800-56522200	Weak transcription	Hela-S3	cervix
21	chr15:56515800-56522400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr15:56515800-56523200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr15:56515800-56523800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr15:56515800-56523800	Weak transcription	Left Ventricle	heart
25	chr15:56515800-56523800	Weak transcription	Small Intestine	intestine
26	chr15:56515800-56523800	Weak transcription	HepG2	liver
27	chr15:56515800-56524000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr15:56515800-56524200	Weak transcription	HUVEC	blood vessel
29	chr15:56515800-56529200	Weak transcription	Colon Smooth Muscle	Colon
30	chr15:56516200-56525600	Weak transcription	NHDF-Ad	bronchial
31	chr15:56517200-56524200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr15:56517200-56524200	Weak transcription	Rectal Smooth Muscle	rectum
33	chr15:56518600-56527400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr15:56519400-56528400	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr15:56519600-56524600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr15:56519800-56522200	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr15:56519800-56522400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr15:56519800-56523200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr15:56520000-56524200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr15:56520000-56527200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr15:56520200-56530200	ZNF genes & repeats	Dnd41	blood
42	chr15:56520400-56522800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr15:56520400-56523800	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr15:56520400-56525400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
45	chr15:56520400-56525800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
46	chr15:56520400-56526000	ZNF genes & repeats	Brain Germinal Matrix	brain
47	chr15:56520400-56526600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
48	chr15:56520400-56526800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr15:56520400-56527400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
50	chr15:56520600-56526400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain

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