Variant report

Variant	rs16858237
Chromosome Location	chr3:111258529-111258530
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	SMC3	chr3:111258265-111258968	GM12878	blood:	n/a	chr3:111258746-111258760
2	RAD21	chr3:111258478-111258939	ECC-1	luminal epithelium:	n/a	chr3:111258742-111258761 chr3:111258745-111258758 chr3:111258746-111258756 chr3:111258744-111258756
3	RAD21	chr3:111258039-111259199	SK-N-SH	brain:	n/a	chr3:111258742-111258761 chr3:111258745-111258758 chr3:111258746-111258756 chr3:111258744-111258756
4	RAD21	chr3:111258412-111259026	H1-hESC	embryonic stem cell:	n/a	chr3:111258742-111258761 chr3:111258745-111258758 chr3:111258746-111258756 chr3:111258744-111258756
5	MXI1	chr3:111258041-111258831	GM12878	blood:	n/a	n/a
6	RAD21	chr3:111258386-111258899	SK-N-SH_RA	brain:	n/a	chr3:111258742-111258761 chr3:111258745-111258758 chr3:111258746-111258756 chr3:111258744-111258756
7	RAD21	chr3:111258447-111258968	ECC-1	luminal epithelium:	n/a	chr3:111258742-111258761 chr3:111258745-111258758 chr3:111258746-111258756 chr3:111258744-111258756
8	CTCF	chr3:111258422-111259061	HCT-116	colon:	n/a	chr3:111258744-111258762 chr3:111258746-111258759
9	RAD21	chr3:111258308-111259020	A549	lung:	n/a	chr3:111258742-111258761 chr3:111258745-111258758 chr3:111258746-111258756 chr3:111258744-111258756
10	RAD21	chr3:111258493-111258866	MCF-7	breast:	n/a	chr3:111258742-111258761 chr3:111258745-111258758 chr3:111258746-111258756 chr3:111258744-111258756
11	RAD21	chr3:111258253-111259141	HCT-116	colon:	n/a	chr3:111258742-111258761 chr3:111258745-111258758 chr3:111258746-111258756 chr3:111258744-111258756
12	EP300	chr3:111257664-111258828	GM12878	blood:	n/a	chr3:111258305-111258314
13	CTCF	chr3:111258502-111259041	MCF-7	breast:	n/a	chr3:111258744-111258762 chr3:111258746-111258759
14	RAD21	chr3:111258528-111258820	GM12878	blood:	n/a	chr3:111258742-111258761 chr3:111258745-111258758 chr3:111258746-111258756 chr3:111258744-111258756
15	CTCF	chr3:111258234-111259224	A549	lung:	n/a	chr3:111258744-111258762 chr3:111258746-111258759
16	CTCF	chr3:111258487-111258901	H1-hESC	embryonic stem cell:	n/a	chr3:111258744-111258762 chr3:111258746-111258759
17	RAD21	chr3:111258403-111259010	HepG2	liver:	n/a	chr3:111258742-111258761 chr3:111258745-111258758 chr3:111258746-111258756 chr3:111258744-111258756
18	RAD21	chr3:111258469-111259133	MCF-7	breast:	n/a	chr3:111258742-111258761 chr3:111258745-111258758 chr3:111258746-111258756 chr3:111258744-111258756
19	STAT3	chr3:111258253-111258826	GM12878	blood:	n/a	n/a
20	RCOR1	chr3:111257934-111258876	GM12878	blood:	n/a	n/a
21	CTCF	chr3:111257784-111259171	SK-N-SH	brain:	n/a	chr3:111258744-111258762 chr3:111258746-111258759
22	SMC3	chr3:111258188-111259060	SK-N-SH	brain:	n/a	chr3:111258746-111258760
23	CTCF	chr3:111258529-111258922	HepG2	liver:	n/a	chr3:111258744-111258762 chr3:111258746-111258759
24	RAD21	chr3:111258529-111258942	Hela-S3	cervix:	n/a	chr3:111258742-111258761 chr3:111258745-111258758 chr3:111258746-111258756 chr3:111258744-111258756
25	RAD21	chr3:111258401-111258938	GM12878	blood:	n/a	chr3:111258742-111258761 chr3:111258745-111258758 chr3:111258746-111258756 chr3:111258744-111258756
26	CTCF	chr3:111258424-111258902	A549	lung:	n/a	chr3:111258744-111258762 chr3:111258746-111258759
27	MAZ	chr3:111258167-111258933	GM12878	blood:	n/a	n/a
28	CTCF	chr3:111258503-111258971	T-47D	breast:	n/a	chr3:111258744-111258762 chr3:111258746-111258759
29	RAD21	chr3:111258380-111259009	A549	lung:	n/a	chr3:111258742-111258761 chr3:111258745-111258758 chr3:111258746-111258756 chr3:111258744-111258756
30	RAD21	chr3:111258462-111258960	H1-hESC	embryonic stem cell:	n/a	chr3:111258742-111258761 chr3:111258745-111258758 chr3:111258746-111258756 chr3:111258744-111258756
31	MAZ	chr3:111258477-111258847	HepG2	liver:	n/a	n/a
32	STAT3	chr3:111258513-111258917	MCF10A-Er-Src	breast:	n/a	n/a
33	RAD21	chr3:111258350-111258971	SK-N-SH_RA	brain:	n/a	chr3:111258742-111258761 chr3:111258745-111258758 chr3:111258746-111258756 chr3:111258744-111258756
34	CTCF	chr3:111258429-111258903	HCT-116	colon:	n/a	chr3:111258744-111258762 chr3:111258746-111258759
35	CTCF	chr3:111258470-111259016	MCF-7	breast:	n/a	chr3:111258744-111258762 chr3:111258746-111258759
36	CUX1	chr3:111257663-111258803	GM12878	blood:	n/a	n/a
37	CHD2	chr3:111258225-111258735	GM12878	blood:	n/a	n/a
38	RAD21	chr3:111258517-111258964	HepG2	liver:	n/a	chr3:111258742-111258761 chr3:111258745-111258758 chr3:111258746-111258756 chr3:111258744-111258756
39	RAD21	chr3:111258343-111259205	HCT-116	colon:	n/a	chr3:111258742-111258761 chr3:111258745-111258758 chr3:111258746-111258756 chr3:111258744-111258756
40	RAD21	chr3:111258446-111258889	H1-hESC	embryonic stem cell:	n/a	chr3:111258742-111258761 chr3:111258745-111258758 chr3:111258746-111258756 chr3:111258744-111258756
41	ELK1	chr3:111258288-111258814	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:110731196..110732172-chr3:111258286..111259261,6	MCF-7	breast:
2	chr3:111018122..111019094-chr3:111258329..111259040,2	MCF-7	breast:
3	chr3:109250886..109251674-chr3:111258322..111259206,2	MCF-7	breast:

Variant related genes	Relation type
CD96	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11928364	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11928649	0.85[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16858215	0.94[AFR][1000 genomes]
rs16858218	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16858221	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16858238	0.82[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16858274	1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes]
rs16858276	0.87[AMR][1000 genomes]
rs16858277	0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes]
rs16858280	0.91[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes]
rs16858281	0.87[AMR][1000 genomes]
rs2276872	1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes]
rs57476687	0.87[AMR][1000 genomes]
rs57590158	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58906230	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60925257	0.87[AMR][1000 genomes]
rs60973340	0.87[AMR][1000 genomes]
rs721335	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72622318	0.87[AMR][1000 genomes]
rs72622319	0.87[AMR][1000 genomes]
rs72622320	0.87[AMR][1000 genomes]
rs72622321	0.87[AMR][1000 genomes]
rs73852803	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73855136	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73855137	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73855138	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73855139	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73855140	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73855144	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73855145	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7629206	0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes]
rs981953	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs981954	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs981955	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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:65 , 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	chr3:111257200-111258600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr3:111257200-111258600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr3:111257200-111258600	Enhancers	Hela-S3	cervix
5	chr3:111257200-111258600	Enhancers	HMEC	breast
6	chr3:111257200-111258600	Enhancers	NH-A	brain
7	chr3:111257200-111258800	Enhancers	Primary hematopoietic stem cells	blood
8	chr3:111257200-111258800	Enhancers	HSMM	muscle
9	chr3:111257200-111259000	Enhancers	NHLF	lung
10	chr3:111257200-111261000	Enhancers	Primary B cells from peripheral blood	blood
11	chr3:111257400-111258600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:111257400-111258600	Enhancers	HSMMtube	muscle
13	chr3:111257400-111258600	Enhancers	NHEK	skin
14	chr3:111257400-111258800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:111257400-111258800	Enhancers	Fetal Lung	lung
16	chr3:111257400-111258800	Enhancers	Ovary	ovary
17	chr3:111257400-111258800	Enhancers	Stomach Mucosa	stomach
18	chr3:111257400-111258800	Enhancers	Spleen	Spleen
19	chr3:111257400-111259000	Flanking Active TSS	Dnd41	blood
20	chr3:111257600-111258600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:111257600-111258600	Enhancers	Fetal Intestine Large	intestine
22	chr3:111257800-111258600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:111257800-111258600	Enhancers	Aorta	Aorta
24	chr3:111257800-111258600	Enhancers	Fetal Heart	heart
25	chr3:111257800-111258600	Enhancers	Placenta Amnion	Placenta Amnion
26	chr3:111257800-111258600	Flanking Active TSS	GM12878-XiMat	blood
27	chr3:111257800-111258800	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr3:111257800-111258800	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr3:111257800-111258800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:111257800-111258800	Enhancers	HepG2	liver
31	chr3:111257800-111259000	Enhancers	Fetal Intestine Small	intestine
32	chr3:111257800-111259400	Flanking Active TSS	Primary T cells from cord blood	blood
33	chr3:111258000-111258600	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr3:111258000-111258800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
35	chr3:111258000-111258800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr3:111258000-111258800	Enhancers	Muscle Satellite Cultured Cells	--
37	chr3:111258000-111260200	Weak transcription	Small Intestine	intestine
38	chr3:111258000-111261200	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr3:111258200-111258600	Active TSS	Primary T cells fromperipheralblood	blood
40	chr3:111258200-111258600	Flanking Active TSS	Fetal Thymus	thymus
41	chr3:111258200-111258800	Flanking Active TSS	Primary B cells from cord blood	blood
42	chr3:111258200-111258800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
43	chr3:111258200-111258800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
44	chr3:111258200-111258800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr3:111258400-111258600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:111258400-111258600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr3:111258400-111258600	Enhancers	Brain Anterior Caudate	brain
48	chr3:111258400-111258600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
49	chr3:111258400-111258600	Flanking Active TSS	A549	lung
50	chr3:111258400-111258800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links