Variant report

Variant	rs2004553
Chromosome Location	chr3:194877959-194877960
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RELA	chr3:194877930-194878519	GM18951	blood:	n/a	n/a
2	RUNX3	chr3:194877907-194878304	GM12878	blood:	n/a	n/a
3	RUNX3	chr3:194877889-194878292	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:194862609..194865401-chr3:194875415..194878786,3	K562	blood:
2	chr3:194877664..194879576-chr3:194883339..194885682,2	MCF-7	breast:

Variant related genes	Relation type
XXYLT1	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10433328	0.84[ASN][1000 genomes]
rs10433329	0.88[ASN][1000 genomes]
rs10433330	0.88[ASN][1000 genomes]
rs10933700	0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10933701	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12491661	0.85[ASN][1000 genomes]
rs2088040	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2088041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2410844	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28613110	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4677662	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4677811	0.88[ASN][1000 genomes]
rs4677814	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs59556963	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59834989	0.82[AMR][1000 genomes]
rs60528401	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6437460	0.85[ASN][1000 genomes]
rs6799346	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs73206648	0.83[ASN][1000 genomes]
rs73206650	0.83[ASN][1000 genomes]
rs73206651	0.88[ASN][1000 genomes]
rs750470	0.90[AFR][1000 genomes]
rs7653355	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs903309	0.83[ASN][1000 genomes]
rs903311	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9809570	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9824084	0.81[AMR][1000 genomes]
rs9825521	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007697	chr3:194554814-195009930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536873	chr3:194554814-195009930	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv997779	chr3:194687093-194885936	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv536874	chr3:194687093-194885936	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
6	nsv1012592	chr3:194814446-194931562	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
7	nsv536875	chr3:194814446-194931562	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
8	nsv1001492	chr3:194814990-194935397	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
9	nsv461126	chr3:194817484-194961888	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
10	nsv592981	chr3:194817484-194961888	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
11	nsv878137	chr3:194822098-194900432	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
12	nsv461127	chr3:194833940-194934634	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
13	nsv592982	chr3:194833940-194934634	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
14	nsv1014826	chr3:194834615-195631793	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
15	nsv536876	chr3:194834615-195631793	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
16	nsv533904	chr3:194868329-195438728	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
17	nsv1009120	chr3:194874494-194974672	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
18	nsv1010168	chr3:194874494-195135790	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers 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
19	nsv536877	chr3:194874494-195135790	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS 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	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194861000-194881000	Weak transcription	Hela-S3	cervix
2	chr3:194862400-194897800	Weak transcription	Dnd41	blood
3	chr3:194868800-194885400	Enhancers	Fetal Muscle Leg	muscle
4	chr3:194871000-194880800	Enhancers	HUVEC	blood vessel
5	chr3:194871400-194887400	Enhancers	Primary hematopoietic stem cells	blood
6	chr3:194871600-194881200	Weak transcription	Liver	Liver
7	chr3:194871800-194878200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr3:194871800-194882800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr3:194872000-194882800	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr3:194872000-194883000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr3:194872000-194883000	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr3:194873000-194884400	Enhancers	Primary B cells from peripheral blood	blood
13	chr3:194873000-194884600	Enhancers	Fetal Thymus	thymus
14	chr3:194873800-194879200	Enhancers	Spleen	Spleen
15	chr3:194874000-194889800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:194874400-194879000	Enhancers	Primary B cells from cord blood	blood
17	chr3:194875200-194879000	Enhancers	Thymus	Thymus
18	chr3:194875800-194878800	Enhancers	GM12878-XiMat	blood
19	chr3:194876000-194880200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:194876200-194878200	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr3:194876200-194878600	Weak transcription	Primary T cells from cord blood	blood
22	chr3:194876200-194879800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr3:194876200-194880200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:194876200-194880200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:194876200-194880200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:194876200-194880200	Weak transcription	HSMMtube	muscle
27	chr3:194876200-194881000	Enhancers	HepG2	liver
28	chr3:194876400-194879600	Weak transcription	NHDF-Ad	bronchial
29	chr3:194876400-194880000	Weak transcription	Placenta	Placenta
30	chr3:194876400-194881200	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr3:194876600-194880000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:194876600-194880200	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr3:194876600-194880400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:194876600-194880800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:194876600-194881000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:194876600-194893000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr3:194876800-194878200	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr3:194876800-194880000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr3:194876800-194880000	Weak transcription	Osteobl	bone
40	chr3:194876800-194880200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:194876800-194880200	Weak transcription	Fetal Kidney	kidney
42	chr3:194876800-194880200	Weak transcription	K562	blood
43	chr3:194876800-194880800	Weak transcription	HSMM	muscle
44	chr3:194876800-194881400	Weak transcription	Esophagus	oesophagus
45	chr3:194876800-194893800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr3:194877000-194878200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:194877000-194878200	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr3:194877000-194880000	Weak transcription	Small Intestine	intestine
49	chr3:194877000-194880200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr3:194877000-194880200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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