Variant report

Variant	rs62044082
Chromosome Location	chr15:56402082-56402083
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11629483	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11631191	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12905899	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12907263	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12911094	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12911427	0.88[EUR][1000 genomes]
rs12914260	0.82[EUR][1000 genomes]
rs1372753	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1442640	0.88[EUR][1000 genomes]
rs1829542	0.81[ASN][1000 genomes]
rs2119937	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2414464	0.81[ASN][1000 genomes]
rs2682044	0.81[ASN][1000 genomes]
rs2713938	0.81[ASN][1000 genomes]
rs2713941	0.81[ASN][1000 genomes]
rs34044869	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34144128	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34224072	0.88[EUR][1000 genomes]
rs34386737	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34756325	0.80[ASN][1000 genomes]
rs35082998	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35722267	0.84[EUR][1000 genomes]
rs35749329	0.83[EUR][1000 genomes]
rs35972806	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4310791	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4310792	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4774231	0.87[EUR][1000 genomes]
rs4774232	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4774847	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59432349	0.83[EUR][1000 genomes]
rs62044110	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62044111	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6493835	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7165270	0.89[EUR][1000 genomes]
rs7168319	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7174823	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7175745	0.89[EUR][1000 genomes]
rs7496025	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8024031	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8028353	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8029114	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8032242	0.85[EUR][1000 genomes]
rs8033653	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9672886	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9672928	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761872	chr15:56211065-56426501	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	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
3	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
4	esv3425705	chr15:56401685-56404533	Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs62044082	RFX7	cis	Skin Sun Exposed Lower leg	GTEx
rs62044082	RFX7	cis	Adipose Subcutaneous	GTEx
rs62044082	RFX7	cis	lung	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56385600-56405600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:56388800-56403400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr15:56388800-56411600	Weak transcription	Fetal Stomach	stomach
4	chr15:56388800-56414400	Weak transcription	Thymus	Thymus
5	chr15:56388800-56418400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr15:56388800-56433000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr15:56388800-56437200	Weak transcription	Pancreas	Pancrea
8	chr15:56388800-56441600	Weak transcription	Lung	lung
9	chr15:56389400-56407600	Weak transcription	Brain Substantia Nigra	brain
10	chr15:56389400-56418400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr15:56389400-56418400	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr15:56389600-56414400	Weak transcription	HSMMtube	muscle
13	chr15:56389800-56415600	Weak transcription	Placenta	Placenta
14	chr15:56390000-56405600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr15:56390000-56405600	Weak transcription	Fetal Intestine Small	intestine
16	chr15:56390400-56414400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr15:56390600-56412600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr15:56390600-56413200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr15:56390600-56414200	Weak transcription	Fetal Lung	lung
20	chr15:56390600-56414200	Weak transcription	Left Ventricle	heart
21	chr15:56390600-56414600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr15:56390600-56416400	Weak transcription	HUVEC	blood vessel
23	chr15:56390600-56417400	Weak transcription	Adipose Nuclei	Adipose
24	chr15:56390600-56418000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr15:56390800-56418600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr15:56391000-56411800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr15:56391200-56407200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr15:56391800-56415800	Weak transcription	Ovary	ovary
29	chr15:56392600-56417200	Weak transcription	Brain Hippocampus Middle	brain
30	chr15:56393800-56412400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr15:56394000-56405600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr15:56394000-56414200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr15:56394000-56418200	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr15:56394200-56407800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr15:56394200-56417000	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr15:56394400-56411000	Weak transcription	Liver	Liver
37	chr15:56394400-56411600	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr15:56394400-56414000	Weak transcription	HMEC	breast
39	chr15:56394400-56414200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr15:56394400-56414200	Weak transcription	NH-A	brain
41	chr15:56394800-56414800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr15:56395000-56407400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr15:56395000-56411600	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr15:56395000-56412600	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr15:56395000-56415800	Weak transcription	Fetal Thymus	thymus
46	chr15:56395000-56418200	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr15:56395200-56403800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr15:56395200-56414200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr15:56395600-56411400	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr15:56395800-56404800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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