Variant report

Variant	rs58042962
Chromosome Location	chr17:18169947-18169948
allele	A/G
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	chr17:18169887-18175074	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr17:18169868-18170079	U87	brain:	n/a	n/a
3	POLR2A	chr17:18169868-18170088	U87	brain:	n/a	n/a
4	POLR2A	chr17:18169917-18170296	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr17:18169876-18170380	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr17:18169886-18170360	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:18165289..18167460-chr17:18167683..18170089,2	K562	blood:
2	chr17:18168228..18170027-chr17:18171044..18172920,2	K562	blood:
3	chr17:18159414..18161817-chr17:18169101..18171467,2	K562	blood:

Variant related genes	Relation type
ENSG00000260647	TF binding region
ENSG00000177731	Chromatin interaction
ENSG00000260647	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11555081	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12601400	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12601687	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12602780	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12603682	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12603700	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17732686	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17805907	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17806489	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2273026	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2294914	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3088175	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3794773	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3889402	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4925157	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55793748	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55912774	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55940735	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56074845	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56159325	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56230317	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56355515	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56360702	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57476545	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60435159	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67826234	0.97[ASN][1000 genomes]
rs68165736	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7216214	0.85[ASN][1000 genomes]
rs7217566	0.84[ASN][1000 genomes]
rs72831943	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs73289931	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73289935	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73289939	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73289960	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv907776	chr17:18122485-18170948	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
10	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs58042962	SHMT1	cis	Whole Blood	GTEx
rs58042962	SMCR7	cis	Muscle Skeletal	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18164800-18170200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr17:18165000-18176600	Weak transcription	HUVEC	blood vessel
3	chr17:18165200-18175400	Weak transcription	Fetal Kidney	kidney
4	chr17:18165200-18176400	Weak transcription	K562	blood
5	chr17:18165400-18170800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr17:18165400-18171400	Weak transcription	NH-A	brain
7	chr17:18165400-18177600	Weak transcription	Small Intestine	intestine
8	chr17:18165600-18181400	Weak transcription	Psoas Muscle	Psoas
9	chr17:18165800-18170200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr17:18165800-18171400	Strong transcription	Fetal Stomach	stomach
11	chr17:18165800-18173400	Weak transcription	HSMM	muscle
12	chr17:18165800-18175800	Weak transcription	GM12878-XiMat	blood
13	chr17:18165800-18182800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr17:18166000-18173600	Weak transcription	Hela-S3	cervix
15	chr17:18166000-18179600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr17:18166000-18183800	Weak transcription	Fetal Brain Male	brain
17	chr17:18166200-18171400	Strong transcription	Brain Germinal Matrix	brain
18	chr17:18166200-18183600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr17:18166400-18170200	Strong transcription	Brain Inferior Temporal Lobe	brain
20	chr17:18166400-18170400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr17:18166400-18170400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr17:18166400-18182600	Strong transcription	Fetal Brain Female	brain
23	chr17:18166600-18170200	Strong transcription	Fetal Muscle Trunk	muscle
24	chr17:18166600-18171000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
25	chr17:18166800-18170400	Strong transcription	Fetal Muscle Leg	muscle
26	chr17:18167000-18188200	Weak transcription	Stomach Mucosa	stomach
27	chr17:18167200-18171000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr17:18168600-18170800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr17:18168600-18171000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr17:18168600-18171400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr17:18168600-18171400	Weak transcription	HMEC	breast
32	chr17:18168600-18173400	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr17:18168800-18171000	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr17:18168800-18171200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr17:18168800-18171400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr17:18168800-18171400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr17:18168800-18171400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr17:18168800-18171600	Weak transcription	Osteobl	bone
39	chr17:18168800-18173400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr17:18168800-18173600	Weak transcription	A549	lung
41	chr17:18168800-18174000	Weak transcription	Dnd41	blood
42	chr17:18168800-18176400	Weak transcription	Primary B cells from cord blood	blood
43	chr17:18168800-18177600	Weak transcription	Rectal Smooth Muscle	rectum
44	chr17:18168800-18179200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
45	chr17:18168800-18179400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr17:18168800-18183200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr17:18169000-18170000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr17:18169000-18170600	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr17:18169000-18170800	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr17:18169000-18170800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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