Variant report

Variant	rs9903403
Chromosome Location	chr17:18122471-18122472
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:18121617..18124692-chr17:18126477..18129347,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000131899	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12051649	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2075657	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2075658	0.83[EUR][1000 genomes]
rs2245430	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2473656	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2605133	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2856289	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4925144	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59588957	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs712271	0.84[EUR][1000 genomes]
rs712274	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72831919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs854773	0.84[EUR][1000 genomes]
rs854774	0.84[EUR][1000 genomes]
rs854777	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs854778	0.84[EUR][1000 genomes]
rs854780	0.83[EUR][1000 genomes]
rs854783	0.83[EUR][1000 genomes]
rs854796	0.93[ASN][1000 genomes]
rs854800	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs854802	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs854803	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9899249	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9903591	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9913262	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv482491	chr17:17959577-18153920	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv1062828	chr17:18098110-18136330	Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
8	nsv543245	chr17:18098110-18136330	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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
12	nsv543246	chr17:18121007-18165604	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
13	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9903403	SHMT1	cis	Muscle Skeletal	GTEx
rs9903403	SHMT1	cis	Esophagus Muscularis	GTEx
rs9903403	SHMT1	cis	Whole Blood	GTEx
rs9903403	SHMT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:18112600-18127400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr17:18113000-18128200	Weak transcription	Small Intestine	intestine
3	chr17:18113200-18128200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr17:18113600-18128000	Weak transcription	Colon Smooth Muscle	Colon
5	chr17:18113800-18124400	Weak transcription	Hela-S3	cervix
6	chr17:18113800-18124600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr17:18113800-18127400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr17:18113800-18127400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr17:18113800-18128200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr17:18114200-18127400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr17:18114200-18127400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr17:18114200-18127400	Weak transcription	Left Ventricle	heart
13	chr17:18114400-18127400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr17:18114400-18128200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr17:18114600-18123800	Weak transcription	GM12878-XiMat	blood
16	chr17:18114600-18124400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr17:18114600-18124400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr17:18114600-18124400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr17:18114600-18124400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr17:18114600-18124400	Weak transcription	HMEC	breast
21	chr17:18114600-18124400	Weak transcription	HSMM	muscle
22	chr17:18114600-18124600	Weak transcription	A549	lung
23	chr17:18114600-18127400	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr17:18114600-18127800	Weak transcription	Right Ventricle	heart
25	chr17:18114600-18127800	Weak transcription	Spleen	Spleen
26	chr17:18114600-18128000	Weak transcription	Brain Germinal Matrix	brain
27	chr17:18114600-18128000	Weak transcription	Fetal Brain Female	brain
28	chr17:18114600-18128000	Weak transcription	Lung	lung
29	chr17:18114600-18128000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr17:18114600-18128200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr17:18114600-18128200	Weak transcription	Liver	Liver
32	chr17:18114600-18128200	Weak transcription	Brain Angular Gyrus	brain
33	chr17:18114600-18128200	Weak transcription	Brain Anterior Caudate	brain
34	chr17:18114600-18128200	Weak transcription	Brain Cingulate Gyrus	brain
35	chr17:18114600-18128200	Weak transcription	Duodenum Mucosa	Duodenum
36	chr17:18114600-18128200	Weak transcription	Esophagus	oesophagus
37	chr17:18114600-18128200	Weak transcription	Thymus	Thymus
38	chr17:18114600-18128200	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr17:18114600-18128400	Weak transcription	Ovary	ovary
40	chr17:18114600-18128400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr17:18114800-18127400	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr17:18114800-18128200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr17:18114800-18128200	Weak transcription	Fetal Thymus	thymus
44	chr17:18114800-18128400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr17:18115200-18127600	Weak transcription	Fetal Intestine Small	intestine
46	chr17:18116000-18127800	Weak transcription	Pancreas	Pancrea
47	chr17:18116200-18128200	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr17:18117400-18127400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr17:18117600-18127400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr17:18120600-18122800	Enhancers	Fetal Muscle Leg	muscle

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