Variant report

Variant	rs11629483
Chromosome Location	chr15:56459271-56459272
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:56449170..56452087-chr15:56458652..56461237,3	K562	blood:
2	chr15:56452674..56455465-chr15:56458402..56460158,2	K562	blood:

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11631191	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12905899	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12907263	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12911094	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12911427	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12914260	0.82[EUR][1000 genomes]
rs12914640	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1372753	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1442640	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1829542	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2119937	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2414464	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2460647	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2460648	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2460650	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2682044	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2682046	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2682049	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2682051	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2682053	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2682054	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2713923	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2713924	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2713926	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2713933	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2713936	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2713938	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2713941	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2718915	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2718941	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2725870	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34044869	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34144128	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34224072	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34386737	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34756325	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35082998	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35722267	0.82[EUR][1000 genomes]
rs35749329	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35972806	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4310791	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4310792	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4774231	0.86[EUR][1000 genomes]
rs4774232	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4774847	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4774848	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59432349	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62044082	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62044110	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62044111	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493835	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7165270	0.87[EUR][1000 genomes]
rs7168319	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7174823	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7175745	0.87[EUR][1000 genomes]
rs7496025	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8024031	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8028353	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8029114	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8032242	0.85[EUR][1000 genomes]
rs8033653	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9672886	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9672928	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[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
rs11629483	RFX7	cis	Adipose Subcutaneous	GTEx
rs11629483	RFX7	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:96 , 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	chr15:56435400-56461000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr15:56435400-56462400	Weak transcription	Fetal Thymus	thymus
4	chr15:56435400-56465200	Weak transcription	Thymus	Thymus
5	chr15:56441000-56461400	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr15:56442000-56462600	Weak transcription	HSMM	muscle
7	chr15:56442600-56470600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr15:56442800-56462600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr15:56443200-56462600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr15:56446600-56468400	Weak transcription	Fetal Lung	lung
11	chr15:56448400-56460200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr15:56452200-56460800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr15:56453000-56460800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr15:56453000-56463200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr15:56453000-56479600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr15:56453200-56462000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr15:56453200-56465000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr15:56453400-56463400	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr15:56453600-56515000	Weak transcription	NHLF	lung
20	chr15:56453800-56463000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr15:56454000-56462800	Weak transcription	Brain Germinal Matrix	brain
22	chr15:56454000-56464600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr15:56454200-56460600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr15:56454200-56465000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr15:56454400-56462600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr15:56454400-56462600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr15:56454400-56462600	Weak transcription	A549	lung
28	chr15:56454400-56463000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr15:56454400-56464200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr15:56454400-56465000	Weak transcription	Fetal Stomach	stomach
31	chr15:56454400-56465600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr15:56454400-56466400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr15:56454400-56467000	Weak transcription	Brain Angular Gyrus	brain
34	chr15:56454400-56467200	Weak transcription	Brain Cingulate Gyrus	brain
35	chr15:56454400-56470000	Weak transcription	Colon Smooth Muscle	Colon
36	chr15:56454400-56470200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr15:56454400-56473400	Weak transcription	K562	blood
38	chr15:56454600-56463400	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr15:56454600-56463400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr15:56454600-56465600	Weak transcription	Brain Substantia Nigra	brain
41	chr15:56454600-56484000	Weak transcription	Brain Anterior Caudate	brain
42	chr15:56454800-56465200	Weak transcription	Fetal Muscle Trunk	muscle
43	chr15:56455200-56460800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr15:56455400-56462400	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr15:56456000-56460400	Weak transcription	Osteobl	bone
46	chr15:56456000-56463400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr15:56456200-56460000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr15:56456200-56462800	Weak transcription	Liver	Liver
49	chr15:56456600-56464800	Weak transcription	Stomach Smooth Muscle	stomach
50	chr15:56456600-56484800	Weak transcription	Aorta	Aorta

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