Variant report

Variant	rs10900321
Chromosome Location	chr1:146629916-146629917
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:146629903..146632085-chr1:146634779..146636837,2	K562	blood:
2	chr1:146629607..146632064-chr1:146712714..146714253,2	MCF-7	breast:
3	chr1:146628045..146631662-chr1:146631941..146634475,3	K562	blood:
4	chr1:146555657..146558762-chr1:146628491..146630489,3	K562	blood:
5	chr1:146628359..146631144-chr1:146632569..146636227,4	K562	blood:
6	chr1:146554695..146558873-chr1:146629314..146633938,5	MCF-7	breast:
7	chr1:146622097..146624965-chr1:146629211..146630728,2	K562	blood:
8	chr1:146628338..146632381-chr1:146638568..146643066,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000230832	Chromatin interaction
ENSG00000131791	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];1.00[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];0.99[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];0.82[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];0.82[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];0.87[CHD][hapmap]
rs10900315	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10900322	0.82[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];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1442758	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[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];0.82[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];0.87[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs1837983	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[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];0.85[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	0.83[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];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4950380	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6538	0.82[CHD][hapmap]
rs6593738	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.82[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];1.00[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	0.87[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];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6687016	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6689155	0.88[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	0.82[AMR][1000 genomes]
rs7523685	0.82[CHD][hapmap]
rs7552010	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs930495	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]

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
rs10900321	RP11-337C18.8	cis	Artery Tibial	GTEx
rs10900321	CHD1L	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:146619200-146630600	Weak transcription	Gastric	stomach
2	chr1:146622800-146630000	Weak transcription	Small Intestine	intestine
3	chr1:146623400-146630400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:146623400-146630600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr1:146624000-146630600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:146624000-146631800	Weak transcription	Esophagus	oesophagus
7	chr1:146624200-146632800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:146624200-146637600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:146624400-146630400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:146624400-146636000	Strong transcription	Skeletal Muscle Female	skeletal muscle
11	chr1:146624600-146630600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:146624600-146632200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:146624600-146634400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr1:146624600-146639600	Strong transcription	Primary T cells from cord blood	blood
15	chr1:146624600-146640400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr1:146624800-146630000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:146624800-146632800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr1:146624800-146635000	Strong transcription	Primary B cells from cord blood	blood
19	chr1:146624800-146637600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:146624800-146642600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:146625000-146630200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr1:146625000-146634200	Strong transcription	Adipose Nuclei	Adipose
23	chr1:146625000-146638400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:146625000-146638400	Strong transcription	Duodenum Mucosa	Duodenum
25	chr1:146625200-146632800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:146625200-146633800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:146625200-146638200	Strong transcription	Osteobl	bone
28	chr1:146625200-146638600	Strong transcription	Fetal Muscle Leg	muscle
29	chr1:146625200-146639600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr1:146625200-146639600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:146625200-146639800	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr1:146625400-146632800	Strong transcription	NHEK	skin
33	chr1:146625400-146633800	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr1:146625400-146634400	Strong transcription	Fetal Muscle Trunk	muscle
35	chr1:146625400-146635000	Strong transcription	NH-A	brain
36	chr1:146625400-146635400	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr1:146625400-146638200	Strong transcription	HepG2	liver
38	chr1:146625400-146638800	Strong transcription	Liver	Liver
39	chr1:146625400-146639200	Strong transcription	Dnd41	blood
40	chr1:146625400-146639400	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr1:146625600-146633800	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr1:146625600-146639200	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr1:146625800-146630000	Weak transcription	Pancreas	Pancrea
44	chr1:146625800-146635400	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr1:146625800-146639600	Strong transcription	Primary B cells from peripheral blood	blood
46	chr1:146626000-146633800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:146626200-146630200	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr1:146626200-146639600	Weak transcription	Fetal Heart	heart
49	chr1:146626400-146630000	Weak transcription	A549	lung
50	chr1:146626400-146630400	Weak transcription	Brain Inferior Temporal Lobe	brain

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