Variant report

Variant	rs12905899
Chromosome Location	chr15:56449617-56449618
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:56447230..56450204-chr15:56462832..56464767,2	K562	blood:
2	chr15:56448755..56450713-chr15:56452777..56455848,3	K562	blood:
3	chr15:56449170..56452087-chr15:56458652..56461237,3	K562	blood:

Extended variants
information (count: 73 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11629483	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11631191	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12907263	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12911094	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12911427	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]
rs12914260	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12914640	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1372753	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1442640	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1829542	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2119937	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2249090	0.92[CEU][hapmap]
rs2414464	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2460647	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2460648	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2460650	1.00[CEU][hapmap]
rs2682044	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2682046	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs2682051	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2682053	0.80[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2682054	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2682059	0.96[CEU][hapmap]
rs2713923	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2713924	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2713926	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2713933	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.81[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];0.81[AMR][1000 genomes]
rs2713938	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2713941	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2718915	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2718921	0.88[YRI][hapmap]
rs2718934	1.00[CEU][hapmap]
rs2718941	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]
rs2725854	0.96[CEU][hapmap];0.87[YRI][hapmap]
rs2725870	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2947021	0.92[CEU][hapmap]
rs34044869	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34144128	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34224072	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34386737	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34756325	0.87[ASN][1000 genomes]
rs35082998	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35722267	0.89[EUR][1000 genomes]
rs35749329	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35972806	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4310791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4310792	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4774231	0.93[EUR][1000 genomes]
rs4774232	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4774847	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4774848	0.85[ASN][1000 genomes]
rs59432349	0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62044082	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62044110	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62044111	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6493835	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7165270	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7168319	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7174823	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7175745	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7176107	0.80[CEU][hapmap]
rs7496025	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8024031	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8028353	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8029114	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8032242	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8033653	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9672886	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9672928	0.83[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12905899	RFX7	cis	Adipose Subcutaneous	GTEx
rs12905899	FLJ12994	cis	multi-tissue	Pritchard
rs12905899	RFX7	cis	Skin Sun Exposed Lower leg	GTEx
rs12905899	RFX7	cis	lung	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56424800-56453800	Weak transcription	Brain Substantia Nigra	brain
2	chr15:56433800-56464000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr15:56435200-56458800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr15:56435400-56461000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:56435400-56462400	Weak transcription	Fetal Thymus	thymus
6	chr15:56435400-56465200	Weak transcription	Thymus	Thymus
7	chr15:56435800-56454000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr15:56436000-56458000	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr15:56436400-56455800	Weak transcription	Liver	Liver
10	chr15:56436600-56458800	Weak transcription	Primary B cells from cord blood	blood
11	chr15:56441000-56453200	Weak transcription	A549	lung
12	chr15:56441000-56461400	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr15:56442000-56457200	Weak transcription	HMEC	breast
14	chr15:56442000-56458000	Weak transcription	HepG2	liver
15	chr15:56442000-56462600	Weak transcription	HSMM	muscle
16	chr15:56442200-56451000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr15:56442200-56457200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr15:56442600-56470600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr15:56442800-56450800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr15:56442800-56454400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr15:56442800-56462600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr15:56443200-56452200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr15:56443200-56462600	Weak transcription	Duodenum Mucosa	Duodenum
24	chr15:56446600-56468400	Weak transcription	Fetal Lung	lung
25	chr15:56447600-56451200	Weak transcription	Primary hematopoietic stem cells	blood
26	chr15:56447600-56457800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr15:56447800-56455800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr15:56448000-56452200	Weak transcription	Primary T cells from cord blood	blood
29	chr15:56448000-56456400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr15:56448200-56450200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr15:56448200-56458000	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr15:56448400-56460200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr15:56448600-56457800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr15:56449400-56458400	Weak transcription	Dnd41	blood
35	chr15:56449600-56453200	Weak transcription	HUES6 Cell Line	embryonic stem cell

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