Variant report

Variant	rs12603700
Chromosome Location	chr17:18167684-18167685
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:18166767-18169163	Hela-S3	cervix:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:18164305..18167744-chr17:18176383..18179397,3	K562	blood:
2	chr17:18165289..18167460-chr17:18167683..18170089,2	K562	blood:
3	chr17:18127100..18135567-chr17:18158023..18168767,25	MCF-7	breast:
4	chr17:18127732..18129500-chr17:18167269..18169069,2	MCF-7	breast:
5	chr17:18164143..18168210-chr17:18170342..18172063,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000260647	TF binding region
ENSG00000131899	Chromatin interaction
ENSG00000260647	Chromatin interaction
ENSG00000177302	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11555081	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12601400	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12601687	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12602780	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12603682	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17732686	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17805907	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17806489	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2273026	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2294914	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3088175	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3794773	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3889402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925157	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55793748	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55912774	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55940735	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56074845	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56159325	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56230317	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56355515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56360702	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57476545	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58042962	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60435159	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67826234	0.98[ASN][1000 genomes]
rs68165736	0.92[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7216214	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7217566	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72831943	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73289931	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73289935	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73289939	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73289960	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv9503	chr17:18121474-18169166	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
10	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
11	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
rs12603700	SHMT1	cis	Whole Blood	GTEx
rs12603700	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	chr17:18165200-18168200	Weak transcription	Primary B cells from cord blood	blood
4	chr17:18165200-18175400	Weak transcription	Fetal Kidney	kidney
5	chr17:18165200-18176400	Weak transcription	K562	blood
6	chr17:18165400-18170800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr17:18165400-18171400	Weak transcription	NH-A	brain
8	chr17:18165400-18177600	Weak transcription	Small Intestine	intestine
9	chr17:18165600-18168000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr17:18165600-18181400	Weak transcription	Psoas Muscle	Psoas
11	chr17:18165800-18168000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr17:18165800-18169200	Strong transcription	NHEK	skin
13	chr17:18165800-18170200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr17:18165800-18171400	Strong transcription	Fetal Stomach	stomach
15	chr17:18165800-18173400	Weak transcription	HSMM	muscle
16	chr17:18165800-18175800	Weak transcription	GM12878-XiMat	blood
17	chr17:18165800-18182800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr17:18166000-18167800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr17:18166000-18168200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr17:18166000-18168200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr17:18166000-18168800	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr17:18166000-18169000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr17:18166000-18169200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr17:18166000-18169200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr17:18166000-18169200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr17:18166000-18169400	Strong transcription	NHLF	lung
27	chr17:18166000-18169800	Strong transcription	Fetal Intestine Small	intestine
28	chr17:18166000-18173600	Weak transcription	Hela-S3	cervix
29	chr17:18166000-18179600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr17:18166000-18183800	Weak transcription	Fetal Brain Male	brain
31	chr17:18166200-18167800	Weak transcription	HMEC	breast
32	chr17:18166200-18168800	Strong transcription	Rectal Smooth Muscle	rectum
33	chr17:18166200-18168800	Strong transcription	Dnd41	blood
34	chr17:18166200-18169000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr17:18166200-18169000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr17:18166200-18169000	Strong transcription	Brain Anterior Caudate	brain
37	chr17:18166200-18169000	Strong transcription	Ovary	ovary
38	chr17:18166200-18169200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr17:18166200-18169200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr17:18166200-18169200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr17:18166200-18169200	Strong transcription	Fetal Intestine Large	intestine
42	chr17:18166200-18169400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr17:18166200-18169600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr17:18166200-18169600	Strong transcription	Colon Smooth Muscle	Colon
45	chr17:18166200-18169600	Strong transcription	Placenta Amnion	Placenta Amnion
46	chr17:18166200-18171400	Strong transcription	Brain Germinal Matrix	brain
47	chr17:18166200-18183600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr17:18166400-18168000	Genic enhancers	Right Ventricle	heart
49	chr17:18166400-18168600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr17:18166400-18168600	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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