Variant report

Variant	rs7172000
Chromosome Location	chr15:40709579-40709580
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11541642	0.88[EUR][1000 genomes]
rs11557072	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858714	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17671194	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17671250	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17672041	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17733008	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34088794	0.87[EUR][1000 genomes]
rs3803358	0.83[EUR][1000 genomes]
rs55788133	0.87[EUR][1000 genomes]
rs55982218	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164132	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7164321	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7166991	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7169262	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7169404	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8026523	0.86[EUR][1000 genomes]
rs8027487	0.84[EUR][1000 genomes]
rs8033938	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8037207	0.86[EUR][1000 genomes]
rs8040755	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv510660	chr15:40552906-40721883	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs7172000	C15orf23	Cis_1M	lymphoblastoid	RTeQTL
rs7172000	KNSTRN	cis	Nerve Tibial	GTEx
rs7172000	KNSTRN	cis	Whole Blood	GTEx
rs7172000	KNSTRN	cis	Artery Tibial	GTEx
rs7172000	KNSTRN	cis	Muscle Skeletal	GTEx
rs7172000	KNSTRN	cis	Skin Sun Exposed Lower leg	GTEx
rs7172000	KNSTRN	cis	lung	GTEx
rs7172000	KNSTRN	cis	Esophagus Muscularis	GTEx
rs7172000	IVD	cis	Nerve Tibial	GTEx
rs7172000	KNSTRN	cis	Esophagus Mucosa	GTEx
rs7172000	IVD	cis	Esophagus Mucosa	GTEx
rs7172000	IVD	cis	Thyroid	GTEx
rs7172000	KNSTRN	cis	Adipose Subcutaneous	GTEx
rs7172000	IVD	cis	Esophagus Muscularis	GTEx
rs7172000	KNSTRN	cis	Heart Left Ventricle	GTEx
rs7172000	KNSTRN	cis	Artery Aorta	GTEx
rs7172000	IVD	Cis_1M	lymphoblastoid	RTeQTL
rs7172000	IVD	cis	lung	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40698600-40712400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:40698800-40709600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr15:40699000-40714000	Weak transcription	Small Intestine	intestine
4	chr15:40699600-40710000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr15:40699600-40710800	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr15:40699600-40710800	Strong transcription	Primary T cells from cord blood	blood
7	chr15:40699600-40711000	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr15:40699600-40711000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr15:40699600-40711000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr15:40699600-40711200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr15:40699600-40712400	Weak transcription	Right Atrium	heart
12	chr15:40699600-40714000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr15:40699800-40710800	Strong transcription	NHLF	lung
14	chr15:40699800-40711000	Strong transcription	H9 Cell Line	embryonic stem cell
15	chr15:40699800-40711000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:40699800-40711000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr15:40699800-40711000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr15:40699800-40711000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr15:40699800-40711000	Strong transcription	Muscle Satellite Cultured Cells	--
20	chr15:40699800-40711000	Strong transcription	Skeletal Muscle Male	skeletal muscle
21	chr15:40699800-40711000	Strong transcription	Skeletal Muscle Female	skeletal muscle
22	chr15:40699800-40711000	Strong transcription	Osteobl	bone
23	chr15:40699800-40711400	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr15:40699800-40712400	Strong transcription	Fetal Stomach	stomach
25	chr15:40700000-40710600	Strong transcription	HSMM	muscle
26	chr15:40700000-40710800	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr15:40700000-40710800	Strong transcription	Fetal Thymus	thymus
28	chr15:40700000-40711000	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr15:40700000-40711000	Strong transcription	Left Ventricle	heart
30	chr15:40700000-40711000	Strong transcription	Lung	lung
31	chr15:40700000-40711400	Strong transcription	Fetal Muscle Leg	muscle
32	chr15:40700000-40711800	Strong transcription	Thymus	Thymus
33	chr15:40700000-40712200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr15:40700000-40712600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr15:40700200-40710800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr15:40700200-40711000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr15:40700200-40711000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr15:40700200-40711000	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr15:40700200-40711000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr15:40700200-40711000	Strong transcription	Ovary	ovary
41	chr15:40700200-40711200	Strong transcription	Fetal Muscle Trunk	muscle
42	chr15:40700200-40711400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr15:40700200-40711400	Strong transcription	Stomach Smooth Muscle	stomach
44	chr15:40700200-40712600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr15:40700400-40710600	Strong transcription	Brain Substantia Nigra	brain
46	chr15:40700400-40711000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr15:40700400-40711000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr15:40700400-40711000	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr15:40700400-40711000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr15:40700400-40711000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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