Variant report

Variant	rs3088175
Chromosome Location	chr17:18177578-18177579
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:18164305..18167744-chr17:18176383..18179397,3	K562	blood:

Variant related genes	Relation type
ENSG00000177427	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11555081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12601400	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12601687	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12602780	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12603682	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12603700	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1682280	0.80[JPT][hapmap]
rs17732686	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17805907	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17806489	0.87[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2124370	0.84[GIH][hapmap];0.81[JPT][hapmap]
rs2168781	0.81[JPT][hapmap]
rs2273026	0.86[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2290507	0.92[GIH][hapmap];0.81[JPT][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap]
rs2294914	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2461847	0.81[JPT][hapmap]
rs3794773	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3889402	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925145	0.84[GIH][hapmap]
rs4925157	0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925159	0.81[JPT][hapmap]
rs543301	0.87[JPT][hapmap]
rs55793748	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55844190	0.82[EUR][1000 genomes]
rs55912774	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55940735	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56018054	0.82[EUR][1000 genomes]
rs56074845	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56159325	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56230317	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56355515	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56360702	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57476545	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58042962	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs584300	0.81[JPT][hapmap]
rs60435159	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67826234	0.97[ASN][1000 genomes]
rs68165736	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7216214	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7217566	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7222009	0.80[JPT][hapmap]
rs72831943	0.83[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs73289931	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73289935	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73289939	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73289960	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8068517	0.84[GIH][hapmap]
rs8076336	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv1061162	chr17:17978838-18259234	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv492305	chr17:17980441-18424702	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
6	nsv907773	chr17:18099962-18206234	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv907774	chr17:18103907-18206234	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv907775	chr17:18108496-18206234	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv1066718	chr17:18125122-18180807	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
10	nsv833386	chr17:18170261-18332726	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
11	nsv1057081	chr17:18171516-18256347	Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
12	nsv543247	chr17:18171516-18256347	Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3088175	TOP3A	cis	lymphoblastoid	seeQTL
rs3088175	SHMT1	cis	Whole Blood	GTEx
rs3088175	SHMT1	cis	multi-tissue	Pritchard
rs3088175	SMCR7	cis	Muscle Skeletal	GTEx
rs3088175	FLJ36492	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18165400-18177600	Weak transcription	Small Intestine	intestine
2	chr17:18165600-18181400	Weak transcription	Psoas Muscle	Psoas
3	chr17:18165800-18182800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr17:18166000-18179600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr17:18166000-18183800	Weak transcription	Fetal Brain Male	brain
6	chr17:18166200-18183600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr17:18166400-18182600	Strong transcription	Fetal Brain Female	brain
8	chr17:18167000-18188200	Weak transcription	Stomach Mucosa	stomach
9	chr17:18168800-18177600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr17:18168800-18179200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr17:18168800-18179400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr17:18168800-18183200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr17:18169000-18177600	Weak transcription	Aorta	Aorta
14	chr17:18169000-18177600	Weak transcription	Esophagus	oesophagus
15	chr17:18169000-18177600	Weak transcription	Gastric	stomach
16	chr17:18169000-18177600	Weak transcription	Ovary	ovary
17	chr17:18169000-18177600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr17:18169000-18177600	Weak transcription	Right Ventricle	heart
19	chr17:18169000-18181200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr17:18169200-18177600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr17:18169200-18177600	Weak transcription	Left Ventricle	heart
22	chr17:18169200-18177600	Weak transcription	Pancreas	Pancrea
23	chr17:18169200-18179400	Weak transcription	NHDF-Ad	bronchial
24	chr17:18169400-18177600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr17:18171000-18183800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr17:18172000-18177600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr17:18172200-18217400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr17:18172400-18201000	Strong transcription	Fetal Stomach	stomach
29	chr17:18172600-18181800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr17:18172800-18198400	Strong transcription	Thymus	Thymus
31	chr17:18173000-18198400	Strong transcription	Fetal Thymus	thymus
32	chr17:18173000-18199000	Strong transcription	Primary T cells from cord blood	blood
33	chr17:18173000-18200400	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr17:18173000-18213800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr17:18173200-18198400	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr17:18173200-18200200	Strong transcription	Placenta	Placenta
37	chr17:18173400-18183600	Weak transcription	Fetal Heart	heart
38	chr17:18173400-18198200	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr17:18173400-18198400	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr17:18173400-18198800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr17:18173400-18200200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr17:18173400-18200800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr17:18173400-18201000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr17:18173400-18201000	Strong transcription	Fetal Intestine Small	intestine
45	chr17:18173600-18190800	Strong transcription	A549	lung
46	chr17:18173600-18198200	Strong transcription	Stomach Smooth Muscle	stomach
47	chr17:18173600-18200200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr17:18173600-18200800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr17:18174000-18177600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr17:18174000-18200600	Strong transcription	Dnd41	blood

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