Variant report

Variant	rs1556317
Chromosome Location	chr21:46605694-46605695
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:46596742..46598458-chr21:46604486..46606241,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11088982	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11088983	0.91[CEU][hapmap];0.94[CHB][hapmap]
rs12185823	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13047803	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1537121	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1537122	0.81[CEU][hapmap]
rs2150439	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2838778	0.81[JPT][hapmap]
rs2838787	0.81[JPT][hapmap]
rs2838788	0.80[JPT][hapmap]
rs2838791	0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]
rs2838797	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838807	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28782181	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs365791	0.90[ASN][1000 genomes]
rs372766	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs374778	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs377524	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3788180	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs381466	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs384876	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs386762	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs407133	0.80[CEU][hapmap]
rs422720	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs427943	0.81[CEU][hapmap]
rs434492	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs446158	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4819030	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4819031	0.95[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6518214	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7281416	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7281757	0.83[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8126717	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8126895	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8128889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8130224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8133307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8134789	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs983749	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9974232	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv531546	chr21:46504151-47411772	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
3	nsv1059771	chr21:46561482-46830602	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv544481	chr21:46561482-46830602	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv1063943	chr21:46571988-46819424	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv544482	chr21:46571988-46819424	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv1064859	chr21:46571988-46830602	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
8	nsv544483	chr21:46571988-46830602	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers 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	51 gene(s)	inside rSNPs	diseases
9	nsv1061691	chr21:46572641-46831862	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
10	nsv544484	chr21:46572641-46831862	Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
11	esv1802303	chr21:46580319-46606676	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
12	nsv587839	chr21:46580370-46837709	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS 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	51 gene(s)	inside rSNPs	diseases
13	nsv587840	chr21:46580370-46839904	Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
14	nsv916959	chr21:46585681-46831845	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS 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	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1556317	LOC642852	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46583800-46606000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr21:46589000-46606400	Weak transcription	Brain Substantia Nigra	brain
3	chr21:46589000-46646000	Weak transcription	Colonic Mucosa	Colon
4	chr21:46590000-46608800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr21:46590800-46607000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr21:46591400-46605800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr21:46595600-46606000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr21:46595600-46607400	Strong transcription	Muscle Satellite Cultured Cells	--
9	chr21:46595800-46605800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr21:46595800-46607400	Strong transcription	Stomach Smooth Muscle	stomach
11	chr21:46596000-46605800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr21:46596000-46605800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr21:46598600-46606200	Weak transcription	K562	blood
14	chr21:46599600-46607400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr21:46599800-46605800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr21:46600200-46606600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr21:46600400-46606600	Strong transcription	Primary B cells from peripheral blood	blood
18	chr21:46600400-46607200	Weak transcription	Small Intestine	intestine
19	chr21:46601000-46606000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr21:46601200-46606200	Strong transcription	HMEC	breast
21	chr21:46602000-46606400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr21:46603600-46606600	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr21:46603600-46607600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr21:46604000-46605800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr21:46604000-46606000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr21:46604200-46605800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr21:46604200-46606600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr21:46604400-46605800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr21:46604400-46605800	Strong transcription	Adipose Nuclei	Adipose
30	chr21:46604400-46605800	Strong transcription	Fetal Lung	lung
31	chr21:46604400-46605800	Strong transcription	Fetal Muscle Leg	muscle
32	chr21:46604400-46606000	Strong transcription	Fetal Stomach	stomach
33	chr21:46604400-46606200	Strong transcription	Primary T cells from cord blood	blood
34	chr21:46604400-46606200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr21:46604400-46606200	Strong transcription	Fetal Muscle Trunk	muscle
36	chr21:46604400-46606400	Strong transcription	Left Ventricle	heart
37	chr21:46604400-46606600	Strong transcription	Right Ventricle	heart
38	chr21:46604400-46606800	Strong transcription	Ovary	ovary
39	chr21:46604400-46607800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr21:46604600-46605800	Strong transcription	Primary hematopoietic stem cells	blood
41	chr21:46604600-46605800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr21:46604600-46606000	Strong transcription	Aorta	Aorta
43	chr21:46604600-46606400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr21:46604600-46606400	Strong transcription	Colon Smooth Muscle	Colon
45	chr21:46604600-46606400	Strong transcription	HUVEC	blood vessel
46	chr21:46604600-46606400	Strong transcription	Osteobl	bone
47	chr21:46604600-46606600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr21:46604600-46606600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr21:46604600-46606800	Strong transcription	Placenta	Placenta
50	chr21:46604600-46615000	Strong transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links