Variant report

Variant	rs17535381
Chromosome Location	chr15:45669614-45669615
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:45669585-45671424	GM12892	blood:	n/a	n/a
2	POLR2A	chr15:45668632-45671831	GM12891	blood:	n/a	n/a
3	SIN3A	chr15:45669548-45671311	H1-hESC	embryonic stem cell:	n/a	chr15:45670385-45670396 chr15:45670390-45670399
4	POLR2A	chr15:45669574-45671477	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
GATM	TF binding region

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10152337	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10152697	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10851425	1.00[CHB][hapmap]
rs1153830	0.88[CHB][hapmap]
rs1153831	0.88[CHB][hapmap]
rs1153832	0.88[CHB][hapmap]
rs12324848	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1288861	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1288863	1.00[CHB][hapmap]
rs1288865	1.00[CHB][hapmap]
rs16940351	0.91[JPT][hapmap]
rs16941238	1.00[JPT][hapmap]
rs16942066	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16944629	0.88[CHB][hapmap]
rs16952731	0.88[CHB][hapmap]
rs1706799	0.84[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17533116	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17533716	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17537244	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17618294	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2088164	0.88[CHB][hapmap]
rs2433229	0.83[JPT][hapmap]
rs2433600	0.88[CHB][hapmap]
rs2433602	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2453546	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2461706	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2486287	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2668746	0.84[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4448883	0.88[CHB][hapmap]
rs55721266	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55904415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56267974	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56273246	0.96[ASN][1000 genomes]
rs56306977	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56327050	0.96[ASN][1000 genomes]
rs56937414	0.93[ASN][1000 genomes]
rs56967490	0.96[ASN][1000 genomes]
rs57369693	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57419781	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61301536	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6493157	0.88[CHB][hapmap]
rs6493158	0.88[CHB][hapmap]
rs7165838	0.86[CHB][hapmap]
rs7173983	0.88[CHB][hapmap]
rs72709081	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72709084	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72709088	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72709089	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72709092	0.88[AMR][1000 genomes]
rs72711253	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72711255	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72711259	0.96[ASN][1000 genomes]
rs8023437	0.88[CHB][hapmap]
rs8042811	0.88[CHB][hapmap]
rs9972405	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972498	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972528	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv869616	chr15:45401411-45736209	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
5	nsv469721	chr15:45608881-45788002	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv482380	chr15:45608881-45788002	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17535381	CTD-2651B20.4	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45652800-45669800	Weak transcription	Lung	lung
2	chr15:45664400-45669800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr15:45668200-45669800	Enhancers	HSMMtube	muscle
4	chr15:45668400-45669800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr15:45668400-45671200	Bivalent/Poised TSS	Fetal Kidney	kidney
6	chr15:45668600-45669800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr15:45668600-45669800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr15:45668600-45670000	Bivalent Enhancer	Primary B cells from cord blood	blood
9	chr15:45668600-45670400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
10	chr15:45668800-45669800	Weak transcription	Esophagus	oesophagus
11	chr15:45668800-45669800	Enhancers	Stomach Mucosa	stomach
12	chr15:45668800-45669800	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
13	chr15:45668800-45670400	Flanking Active TSS	Duodenum Mucosa	Duodenum
14	chr15:45669000-45669800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
15	chr15:45669000-45669800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr15:45669000-45669800	Enhancers	Colonic Mucosa	Colon
17	chr15:45669000-45669800	Active TSS	Fetal Muscle Trunk	muscle
18	chr15:45669000-45669800	Weak transcription	Psoas Muscle	Psoas
19	chr15:45669000-45669800	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr15:45669000-45669800	Weak transcription	Spleen	Spleen
21	chr15:45669000-45670000	Flanking Active TSS	Fetal Intestine Small	intestine
22	chr15:45669000-45670000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr15:45669000-45670400	Flanking Active TSS	Stomach Smooth Muscle	stomach
24	chr15:45669000-45671200	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr15:45669000-45671200	Active TSS	Ovary	ovary
26	chr15:45669000-45671200	Active TSS	Right Atrium	heart
27	chr15:45669000-45671600	Active TSS	Brain Angular Gyrus	brain
28	chr15:45669000-45671800	Active TSS	Pancreas	Pancrea
29	chr15:45669200-45669800	Bivalent Enhancer	Primary hematopoietic stem cells	blood
30	chr15:45669200-45669800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
31	chr15:45669200-45669800	Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr15:45669200-45670400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
33	chr15:45669200-45670800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
34	chr15:45669200-45671200	Active TSS	Brain Anterior Caudate	brain
35	chr15:45669200-45671200	Active TSS	Brain Hippocampus Middle	brain
36	chr15:45669200-45671400	Active TSS	Brain Inferior Temporal Lobe	brain
37	chr15:45669400-45669800	Enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr15:45669400-45669800	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
39	chr15:45669400-45670000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
40	chr15:45669400-45670000	Bivalent Enhancer	Fetal Thymus	thymus
41	chr15:45669400-45671200	Active TSS	Brain Substantia Nigra	brain
42	chr15:45669400-45671400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
43	chr15:45669400-45675200	Weak transcription	HepG2	liver
44	chr15:45669600-45669800	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
45	chr15:45669600-45669800	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr15:45669600-45669800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr15:45669600-45669800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr15:45669600-45669800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
49	chr15:45669600-45669800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
50	chr15:45669600-45669800	Bivalent Enhancer	Primary B cells from peripheral blood	blood

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