Variant report

Variant	rs56355515
Chromosome Location	chr17:18169244-18169245
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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	Chromatin interaction
ENSG00000177731	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];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12601400	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12601687	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[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];0.80[ASN][1000 genomes]
rs12603700	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17732686	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17805907	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17806489	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2273026	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2294914	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3088175	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3794773	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3889402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4925157	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55793748	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55912774	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55940735	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56074845	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56159325	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56230317	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56360702	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57476545	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58042962	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60435159	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67826234	0.94[ASN][1000 genomes]
rs68165736	0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7216214	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7217566	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72831943	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73289931	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[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];0.98[ASN][1000 genomes]
rs73289960	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[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
rs56355515	SHMT1	cis	Whole Blood	GTEx
rs56355515	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	chr17:18166000-18169400	Strong transcription	NHLF	lung
15	chr17:18166000-18169800	Strong transcription	Fetal Intestine Small	intestine
16	chr17:18166000-18173600	Weak transcription	Hela-S3	cervix
17	chr17:18166000-18179600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr17:18166000-18183800	Weak transcription	Fetal Brain Male	brain
19	chr17:18166200-18169400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr17:18166200-18169600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr17:18166200-18169600	Strong transcription	Colon Smooth Muscle	Colon
22	chr17:18166200-18169600	Strong transcription	Placenta Amnion	Placenta Amnion
23	chr17:18166200-18171400	Strong transcription	Brain Germinal Matrix	brain
24	chr17:18166200-18183600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr17:18166400-18169400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr17:18166400-18169600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr17:18166400-18170200	Strong transcription	Brain Inferior Temporal Lobe	brain
28	chr17:18166400-18170400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr17:18166400-18170400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr17:18166400-18182600	Strong transcription	Fetal Brain Female	brain
31	chr17:18166600-18169600	Strong transcription	Brain Hippocampus Middle	brain
32	chr17:18166600-18170200	Strong transcription	Fetal Muscle Trunk	muscle
33	chr17:18166600-18171000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
34	chr17:18166800-18170400	Strong transcription	Fetal Muscle Leg	muscle
35	chr17:18167000-18169600	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr17:18167000-18188200	Weak transcription	Stomach Mucosa	stomach
37	chr17:18167200-18171000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr17:18168000-18169600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr17:18168600-18170800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr17:18168600-18171000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr17:18168600-18171400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr17:18168600-18171400	Weak transcription	HMEC	breast
43	chr17:18168600-18173400	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr17:18168800-18171000	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr17:18168800-18171200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr17:18168800-18171400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr17:18168800-18171400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr17:18168800-18171400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr17:18168800-18171600	Weak transcription	Osteobl	bone
50	chr17:18168800-18173400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links