Variant report

Variant	rs12911427
Chromosome Location	chr15:56457824-56457825
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs11629483	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11631191	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12905782	0.87[CEU][hapmap]
rs12905899	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12907263	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12911094	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12914260	0.87[EUR][1000 genomes]
rs12914640	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1372753	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]
rs1442640	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1829542	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2119937	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2249090	0.91[CEU][hapmap]
rs2414464	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2460647	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2460648	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2460650	0.96[CEU][hapmap];0.81[AMR][1000 genomes]
rs2682044	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2682046	0.92[ASN][1000 genomes]
rs2682051	0.96[CEU][hapmap];0.83[CHB][hapmap]
rs2682054	0.96[CEU][hapmap]
rs2682059	0.92[CEU][hapmap]
rs2713923	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2713924	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2713926	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2713933	0.96[CEU][hapmap];0.83[CHB][hapmap]
rs2713935	0.84[CHB][hapmap];0.80[JPT][hapmap]
rs2713936	0.96[CEU][hapmap];0.83[CHB][hapmap]
rs2713938	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2713941	0.96[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2718915	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2718934	0.96[CEU][hapmap]
rs2718941	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]
rs2725854	0.92[CEU][hapmap];0.83[CHB][hapmap]
rs2725870	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2947021	0.92[CEU][hapmap]
rs34044869	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34144128	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34224072	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34386737	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34756325	0.87[ASN][1000 genomes]
rs35082998	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35722267	0.86[EUR][1000 genomes]
rs35749329	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35972806	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4310791	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4310792	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4774231	0.91[EUR][1000 genomes]
rs4774232	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4774847	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4774848	0.86[ASN][1000 genomes]
rs59432349	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62044082	0.88[EUR][1000 genomes]
rs62044110	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62044111	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6493835	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7165270	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7168319	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7174823	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7175745	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7496025	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]
rs8024031	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8028353	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8029114	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8032242	0.89[EUR][1000 genomes]
rs8033653	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9672886	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9672928	0.81[JPT][hapmap];0.85[EUR][1000 genomes];0.90[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	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
3	esv1811079	chr15:56448125-56462293	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12911427	RFX7	cis	Adipose Subcutaneous	GTEx
rs12911427	RFX7	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56433800-56464000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr15:56435200-56458800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr15:56435400-56461000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:56435400-56462400	Weak transcription	Fetal Thymus	thymus
5	chr15:56435400-56465200	Weak transcription	Thymus	Thymus
6	chr15:56436000-56458000	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr15:56436600-56458800	Weak transcription	Primary B cells from cord blood	blood
8	chr15:56441000-56461400	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr15:56442000-56458000	Weak transcription	HepG2	liver
10	chr15:56442000-56462600	Weak transcription	HSMM	muscle
11	chr15:56442600-56470600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr15:56442800-56462600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr15:56443200-56462600	Weak transcription	Duodenum Mucosa	Duodenum
14	chr15:56446600-56468400	Weak transcription	Fetal Lung	lung
15	chr15:56448200-56458000	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr15:56448400-56460200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr15:56449400-56458400	Weak transcription	Dnd41	blood
18	chr15:56451200-56458200	Weak transcription	Primary B cells from peripheral blood	blood
19	chr15:56452200-56460800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr15:56452400-56458800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr15:56452400-56458800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr15:56453000-56460800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr15:56453000-56463200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr15:56453000-56479600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr15:56453200-56462000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr15:56453200-56465000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr15:56453400-56463400	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr15:56453600-56515000	Weak transcription	NHLF	lung
29	chr15:56453800-56463000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr15:56454000-56462800	Weak transcription	Brain Germinal Matrix	brain
31	chr15:56454000-56464600	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr15:56454200-56460600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr15:56454200-56465000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr15:56454400-56462600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr15:56454400-56462600	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr15:56454400-56462600	Weak transcription	A549	lung
37	chr15:56454400-56463000	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr15:56454400-56464200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr15:56454400-56465000	Weak transcription	Fetal Stomach	stomach
40	chr15:56454400-56465600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr15:56454400-56466400	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr15:56454400-56467000	Weak transcription	Brain Angular Gyrus	brain
43	chr15:56454400-56467200	Weak transcription	Brain Cingulate Gyrus	brain
44	chr15:56454400-56470000	Weak transcription	Colon Smooth Muscle	Colon
45	chr15:56454400-56470200	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr15:56454400-56473400	Weak transcription	K562	blood
47	chr15:56454600-56458000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr15:56454600-56463400	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr15:56454600-56463400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr15:56454600-56465600	Weak transcription	Brain Substantia Nigra	brain

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