Variant report

Variant	rs930495
Chromosome Location	chr1:146634514-146634515
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	chr1:146632272..146634531-chr1:146713179..146715784,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000131781	Chromatin interaction
ENSG00000131778	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1036850	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1036851	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1036852	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1047140	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10751402	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10793652	0.82[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.85[ASN][1000 genomes]
rs10793653	0.82[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[ASN][1000 genomes]
rs10793656	0.82[CHD][hapmap]
rs10900314	0.82[CHB][hapmap];0.86[CHD][hapmap]
rs10900315	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10900321	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10900322	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10900326	0.82[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1123333	0.92[CEU][hapmap];0.89[GIH][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs11239950	0.85[ASN][1000 genomes]
rs11239951	0.82[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[ASN][1000 genomes]
rs11578109	0.85[ASN][1000 genomes]
rs12028924	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12139680	0.85[ASN][1000 genomes]
rs12144240	0.97[ASN][1000 genomes]
rs1348316	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1442758	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1442760	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1470261	0.92[CEU][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs1470262	0.92[CEU][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs17359526	0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs1837983	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1837984	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1899485	0.86[CHD][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap]
rs2044151	0.87[ASN][1000 genomes]
rs2078325	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs2083719	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2289575	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2354442	0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs4950366	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4950368	0.81[EUR][1000 genomes]
rs4950372	1.00[JPT][hapmap]
rs4950378	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4950380	0.97[ASN][1000 genomes]
rs6538	0.82[CHD][hapmap]
rs6593738	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6593739	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668690	0.83[ASN][1000 genomes]
rs6670503	0.88[CEU][hapmap];0.89[GIH][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs6673185	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6675377	0.82[ASN][1000 genomes]
rs6680845	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6687016	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6689155	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6693631	0.82[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs71510593	0.85[ASN][1000 genomes]
rs7517655	0.81[AMR][1000 genomes]
rs7523685	0.82[CHD][hapmap]
rs7552010	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757753	chr1:145883119-146697542	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv872251	chr1:146152553-146803630	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv872252	chr1:146471863-147398135	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
4	nsv999546	chr1:146507577-147356574	Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
5	nsv535123	chr1:146507577-147356574	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
6	nsv492188	chr1:146507649-147381479	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
7	nsv916754	chr1:146507711-147417736	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
8	nsv547673	chr1:146510112-147398135	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
9	nsv547674	chr1:146522722-147396797	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
10	nsv998341	chr1:146531446-147384720	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
11	nsv535124	chr1:146531446-147384720	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
12	nsv1003493	chr1:146531446-147389944	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
13	nsv998209	chr1:146543722-147384720	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
14	nsv535126	chr1:146543722-147384720	Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
15	nsv872255	chr1:146550780-146969712	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
16	nsv872256	chr1:146556596-147410973	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
17	nsv1012331	chr1:146603479-147384720	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
18	nsv535131	chr1:146603479-147384720	Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
19	nsv1009943	chr1:146618929-146893851	Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
20	nsv535132	chr1:146618929-146893851	Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs930495	RP11-337C18.8	cis	Artery Tibial	GTEx
rs930495	CHD1L	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:146624200-146637600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr1:146624400-146636000	Strong transcription	Skeletal Muscle Female	skeletal muscle
3	chr1:146624600-146639600	Strong transcription	Primary T cells from cord blood	blood
4	chr1:146624600-146640400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr1:146624800-146635000	Strong transcription	Primary B cells from cord blood	blood
6	chr1:146624800-146637600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr1:146624800-146642600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:146625000-146638400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:146625000-146638400	Strong transcription	Duodenum Mucosa	Duodenum
10	chr1:146625200-146638200	Strong transcription	Osteobl	bone
11	chr1:146625200-146638600	Strong transcription	Fetal Muscle Leg	muscle
12	chr1:146625200-146639600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:146625200-146639600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:146625200-146639800	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr1:146625400-146635000	Strong transcription	NH-A	brain
16	chr1:146625400-146635400	Strong transcription	Duodenum Smooth Muscle	Duodenum
17	chr1:146625400-146638200	Strong transcription	HepG2	liver
18	chr1:146625400-146638800	Strong transcription	Liver	Liver
19	chr1:146625400-146639200	Strong transcription	Dnd41	blood
20	chr1:146625400-146639400	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr1:146625600-146639200	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr1:146625800-146635400	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr1:146625800-146639600	Strong transcription	Primary B cells from peripheral blood	blood
24	chr1:146626200-146639600	Weak transcription	Fetal Heart	heart
25	chr1:146627000-146635600	Strong transcription	Fetal Intestine Large	intestine
26	chr1:146627400-146635200	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr1:146627600-146635600	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr1:146627600-146639600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:146628000-146639600	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr1:146628200-146635200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr1:146628800-146634600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:146628800-146635200	Strong transcription	Primary hematopoietic stem cells	blood
33	chr1:146628800-146635200	Strong transcription	Colon Smooth Muscle	Colon
34	chr1:146628800-146639400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr1:146629000-146639400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr1:146629200-146634800	Strong transcription	Stomach Smooth Muscle	stomach
37	chr1:146629200-146635400	Strong transcription	Brain Angular Gyrus	brain
38	chr1:146629200-146635400	Strong transcription	Fetal Lung	lung
39	chr1:146629400-146639400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr1:146629800-146635200	Strong transcription	Brain Germinal Matrix	brain
41	chr1:146629800-146640200	Weak transcription	K562	blood
42	chr1:146630000-146634600	Strong transcription	Right Ventricle	heart
43	chr1:146630000-146641200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr1:146630200-146634800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:146630400-146635000	Strong transcription	HSMM	muscle
46	chr1:146630800-146636600	Weak transcription	Fetal Intestine Small	intestine
47	chr1:146630800-146637600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr1:146630800-146640200	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr1:146631200-146635200	Weak transcription	Fetal Stomach	stomach
50	chr1:146631400-146637400	Weak transcription	Small Intestine	intestine

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