Variant report

Variant	rs17806489
Chromosome Location	chr17:18249611-18249612
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:18248848..18250990-chr17:18266650..18268234,2	K562	blood:
2	chr17:18234071..18236866-chr17:18249384..18251681,2	K562	blood:
3	chr17:18233805..18235571-chr17:18249290..18250884,2	K562	blood:

Variant related genes	Relation type
ENSG00000176974	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11555081	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12601400	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12601687	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12602780	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12603682	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12603700	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1682280	0.80[JPT][hapmap]
rs17732686	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17805907	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2124370	0.88[GIH][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap]
rs2168781	0.81[JPT][hapmap]
rs2273026	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290507	0.96[GIH][hapmap];0.81[JPT][hapmap]
rs2294914	0.87[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2461847	0.81[JPT][hapmap]
rs3088175	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]
rs3794773	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3889402	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4925145	0.88[GIH][hapmap]
rs4925157	0.86[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4925159	0.81[JPT][hapmap]
rs543301	0.87[JPT][hapmap]
rs55793748	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55844190	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55912774	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55940735	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56014455	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs56018054	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56074845	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56159325	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56230317	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56355515	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56360702	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57476545	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58042962	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs584300	0.81[JPT][hapmap]
rs60435159	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6502652	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67826234	0.81[ASN][1000 genomes]
rs68165736	0.81[ASN][1000 genomes]
rs7216214	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7217566	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7222009	0.80[JPT][hapmap]
rs72831943	0.83[ASN][1000 genomes]
rs73289931	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73289935	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73289939	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73289960	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8068517	0.88[GIH][hapmap]
rs8073885	0.88[ASN][1000 genomes]
rs8076336	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	nsv1062368	chr17:18180747-18259234	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv833387	chr17:18200081-18378155	Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS 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	34 gene(s)	inside rSNPs	diseases
9	esv1806346	chr17:18200081-18446384	Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
10	esv1812661	chr17:18200081-18446384	Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
11	nsv428333	chr17:18200081-18446384	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' 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	39 gene(s)	inside rSNPs	diseases
12	nsv427992	chr17:18200081-19192047	Strong transcription Genic enhancers Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
13	esv2758443	chr17:18234525-18446384	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
14	esv2758677	chr17:18234525-18446384	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
15	esv1829832	chr17:18235992-18405148	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17806489	TOP3A	cis	multi-tissue	Pritchard
rs17806489	SHMT1	cis	multi-tissue	Pritchard
rs17806489	FLJ36492	cis	multi-tissue	Pritchard
rs17806489	SMCR7	cis	Muscle Skeletal	GTEx
rs17806489	SHMT1	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18219400-18266000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr17:18222400-18266200	Weak transcription	Small Intestine	intestine
3	chr17:18223600-18265400	Strong transcription	Fetal Stomach	stomach
4	chr17:18223800-18253600	Strong transcription	Thymus	Thymus
5	chr17:18224200-18253000	Weak transcription	Fetal Heart	heart
6	chr17:18228200-18265800	Weak transcription	Fetal Brain Male	brain
7	chr17:18228600-18251400	Weak transcription	HSMMtube	muscle
8	chr17:18228600-18266000	Weak transcription	HSMM	muscle
9	chr17:18229000-18266000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr17:18230000-18260000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr17:18230200-18260200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr17:18230200-18265600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr17:18231000-18266000	Weak transcription	Psoas Muscle	Psoas
14	chr17:18231200-18260600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr17:18235400-18256600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr17:18235800-18265400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr17:18236400-18250000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr17:18236600-18250400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr17:18237600-18260200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr17:18239000-18249800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr17:18239000-18250200	Weak transcription	NHDF-Ad	bronchial
22	chr17:18242200-18260400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr17:18242400-18252200	Strong transcription	H9 Cell Line	embryonic stem cell
24	chr17:18242400-18252400	Strong transcription	HepG2	liver
25	chr17:18242400-18253000	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr17:18242400-18253000	Strong transcription	Adipose Nuclei	Adipose
27	chr17:18242400-18253000	Strong transcription	Duodenum Mucosa	Duodenum
28	chr17:18242400-18258200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr17:18242400-18259600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr17:18242400-18264000	Strong transcription	Fetal Thymus	thymus
31	chr17:18242600-18252200	Strong transcription	Esophagus	oesophagus
32	chr17:18242600-18258200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr17:18242600-18260400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr17:18242800-18257000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr17:18243600-18260400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr17:18243800-18264200	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr17:18244000-18256200	Weak transcription	Colon Smooth Muscle	Colon
38	chr17:18244000-18263800	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr17:18244200-18250200	Weak transcription	Colonic Mucosa	Colon
40	chr17:18244200-18259800	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr17:18244200-18263800	Strong transcription	Fetal Intestine Small	intestine
42	chr17:18244400-18249800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr17:18244400-18252800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr17:18244400-18255200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr17:18244400-18264200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr17:18244400-18264200	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr17:18244400-18266200	Weak transcription	Stomach Mucosa	stomach
48	chr17:18244600-18252400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr17:18244600-18258000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr17:18245400-18266000	Weak transcription	NH-A	brain

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