Variant report

Variant	rs981955
Chromosome Location	chr3:111258206-111258207
allele	C/G
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	RAD21	chr3:111258039-111259199	SK-N-SH	brain:	n/a	chr3:111258742-111258761 chr3:111258745-111258758 chr3:111258746-111258756 chr3:111258744-111258756
2	MXI1	chr3:111258041-111258831	GM12878	blood:	n/a	n/a
3	RUNX3	chr3:111257597-111258510	GM12878	blood:	n/a	chr3:111258274-111258283 chr3:111257847-111257856 chr3:111257847-111257856 chr3:111258274-111258283
4	RUNX3	chr3:111257618-111258477	GM12878	blood:	n/a	chr3:111258274-111258283 chr3:111257847-111257856 chr3:111257847-111257856 chr3:111258274-111258283
5	EP300	chr3:111257664-111258828	GM12878	blood:	n/a	chr3:111258305-111258314
6	EP300	chr3:111257957-111258471	GM12878	blood:	n/a	chr3:111258305-111258314
7	NFIC	chr3:111258058-111258504	GM12878	blood:	n/a	n/a
8	RCOR1	chr3:111257934-111258876	GM12878	blood:	n/a	n/a
9	CTCF	chr3:111257784-111259171	SK-N-SH	brain:	n/a	chr3:111258744-111258762 chr3:111258746-111258759
10	SMC3	chr3:111258188-111259060	SK-N-SH	brain:	n/a	chr3:111258746-111258760
11	MAZ	chr3:111258167-111258933	GM12878	blood:	n/a	n/a
12	EP300	chr3:111257773-111258448	GM12878	blood:	n/a	chr3:111258305-111258314
13	CUX1	chr3:111257663-111258803	GM12878	blood:	n/a	n/a
14	SPI1	chr3:111258193-111258450	GM12878	blood:	n/a	chr3:111258304-111258317 chr3:111258303-111258316 chr3:111258305-111258314

Variant related genes	Relation type
CD96	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11928364	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11928649	0.85[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16858218	1.00[CHB][hapmap];1.00[JPT][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]
rs16858221	1.00[CHB][hapmap];1.00[JPT][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]
rs16858229	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs16858237	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16858238	0.85[CHB][hapmap];0.85[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16858274	0.91[AMR][1000 genomes]
rs16858276	0.91[AMR][1000 genomes]
rs16858277	0.91[AMR][1000 genomes]
rs16858280	0.91[AMR][1000 genomes]
rs16858281	0.91[AMR][1000 genomes]
rs2276872	0.91[AMR][1000 genomes]
rs57476687	0.91[AMR][1000 genomes]
rs57590158	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58085859	0.95[AFR][1000 genomes]
rs58195592	0.95[AFR][1000 genomes]
rs58906230	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60925257	0.91[AMR][1000 genomes]
rs60973340	0.91[AMR][1000 genomes]
rs721335	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72622318	0.91[AMR][1000 genomes]
rs72622319	0.91[AMR][1000 genomes]
rs72622320	0.91[AMR][1000 genomes]
rs72622321	0.91[AMR][1000 genomes]
rs72939542	0.90[AFR][1000 genomes]
rs73852803	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73855128	0.95[AFR][1000 genomes]
rs73855135	0.97[AFR][1000 genomes]
rs73855136	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73855137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73855138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73855139	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73855140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73855144	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73855145	0.96[AMR][1000 genomes]
rs7629206	0.91[AMR][1000 genomes]
rs981953	1.00[CHB][hapmap];1.00[JPT][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]
rs981954	1.00[CHB][hapmap];1.00[JPT][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]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv997756	chr3:111226058-111376585	Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv3946	chr3:111236035-111283038	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111255800-111264400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:111257000-111258400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr3:111257000-111258400	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr3:111257200-111258400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:111257200-111258400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:111257200-111258400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr3:111257200-111258400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr3:111257200-111258400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:111257200-111258400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:111257200-111258400	Enhancers	Osteobl	bone
11	chr3:111257200-111258600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:111257200-111258600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr3:111257200-111258600	Enhancers	Hela-S3	cervix
14	chr3:111257200-111258600	Enhancers	HMEC	breast
15	chr3:111257200-111258600	Enhancers	NH-A	brain
16	chr3:111257200-111258800	Enhancers	Primary hematopoietic stem cells	blood
17	chr3:111257200-111258800	Enhancers	HSMM	muscle
18	chr3:111257200-111259000	Enhancers	NHLF	lung
19	chr3:111257200-111261000	Enhancers	Primary B cells from peripheral blood	blood
20	chr3:111257400-111258400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr3:111257400-111258400	Enhancers	Duodenum Mucosa	Duodenum
22	chr3:111257400-111258400	Enhancers	A549	lung
23	chr3:111257400-111258600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:111257400-111258600	Enhancers	HSMMtube	muscle
25	chr3:111257400-111258600	Enhancers	NHEK	skin
26	chr3:111257400-111258800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:111257400-111258800	Enhancers	Fetal Lung	lung
28	chr3:111257400-111258800	Enhancers	Ovary	ovary
29	chr3:111257400-111258800	Enhancers	Stomach Mucosa	stomach
30	chr3:111257400-111258800	Enhancers	Spleen	Spleen
31	chr3:111257400-111259000	Flanking Active TSS	Dnd41	blood
32	chr3:111257600-111258400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr3:111257600-111258400	Enhancers	Thymus	Thymus
34	chr3:111257600-111258600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:111257600-111258600	Enhancers	Fetal Intestine Large	intestine
36	chr3:111257800-111258400	Enhancers	Liver	Liver
37	chr3:111257800-111258400	Enhancers	Rectal Mucosa Donor 29	rectum
38	chr3:111257800-111258600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:111257800-111258600	Enhancers	Aorta	Aorta
40	chr3:111257800-111258600	Enhancers	Fetal Heart	heart
41	chr3:111257800-111258600	Enhancers	Placenta Amnion	Placenta Amnion
42	chr3:111257800-111258600	Flanking Active TSS	GM12878-XiMat	blood
43	chr3:111257800-111258800	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr3:111257800-111258800	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr3:111257800-111258800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:111257800-111258800	Enhancers	HepG2	liver
47	chr3:111257800-111259000	Enhancers	Fetal Intestine Small	intestine
48	chr3:111257800-111259400	Flanking Active TSS	Primary T cells from cord blood	blood
49	chr3:111258000-111258400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:111258000-111258400	Enhancers	Primary T helper cells PMA-I stimulated	--

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