Variant report

Variant	rs4682049
Chromosome Location	chr3:111259021-111259022
allele	A/C
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	RAD21	chr3:111258412-111259026	H1-hESC	embryonic stem cell:	n/a	chr3:111258742-111258761 chr3:111258745-111258758 chr3:111258746-111258756 chr3:111258744-111258756
3	CTCF	chr3:111258422-111259061	HCT-116	colon:	n/a	chr3:111258744-111258762 chr3:111258746-111258759
4	RAD21	chr3:111258253-111259141	HCT-116	colon:	n/a	chr3:111258742-111258761 chr3:111258745-111258758 chr3:111258746-111258756 chr3:111258744-111258756
5	CTCF	chr3:111258502-111259041	MCF-7	breast:	n/a	chr3:111258744-111258762 chr3:111258746-111258759
6	CTCF	chr3:111258234-111259224	A549	lung:	n/a	chr3:111258744-111258762 chr3:111258746-111258759
7	RAD21	chr3:111258469-111259133	MCF-7	breast:	n/a	chr3:111258742-111258761 chr3:111258745-111258758 chr3:111258746-111258756 chr3:111258744-111258756
8	CTCF	chr3:111257784-111259171	SK-N-SH	brain:	n/a	chr3:111258744-111258762 chr3:111258746-111258759
9	MAZ	chr3:111258534-111259023	IMR90	lung:	n/a	n/a
10	SMC3	chr3:111258188-111259060	SK-N-SH	brain:	n/a	chr3:111258746-111258760
11	RAD21	chr3:111258343-111259205	HCT-116	colon:	n/a	chr3:111258742-111258761 chr3:111258745-111258758 chr3:111258746-111258756 chr3:111258744-111258756

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: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10511299	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12633539	0.98[ASN][1000 genomes]
rs13087173	0.99[ASN][1000 genomes]
rs13087579	0.99[ASN][1000 genomes]
rs1398748	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs2173318	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2276873	0.91[JPT][hapmap];0.85[YRI][hapmap];0.89[ASN][1000 genomes]
rs6792149	0.81[ASN][1000 genomes]
rs7628039	0.82[JPT][hapmap]
rs7653347	0.91[JPT][hapmap];0.85[YRI][hapmap];0.89[ASN][1000 genomes]
rs9865195	0.82[JPT][hapmap]

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:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111255800-111264400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:111257200-111261000	Enhancers	Primary B cells from peripheral blood	blood
3	chr3:111257800-111259400	Flanking Active TSS	Primary T cells from cord blood	blood
4	chr3:111258000-111260200	Weak transcription	Small Intestine	intestine
5	chr3:111258000-111261200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:111258600-111259200	Enhancers	GM12878-XiMat	blood
7	chr3:111258600-111260000	Weak transcription	NH-A	brain
8	chr3:111258600-111260600	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr3:111258600-111260600	Enhancers	Fetal Thymus	thymus
10	chr3:111258600-111260800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:111258600-111265200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:111258600-111266800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:111258800-111259200	Enhancers	Primary B cells from cord blood	blood
14	chr3:111258800-111259200	Enhancers	Primary T cells fromperipheralblood	blood
15	chr3:111258800-111259400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr3:111258800-111259600	Enhancers	Thymus	Thymus
17	chr3:111258800-111259800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr3:111258800-111260000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr3:111258800-111260000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr3:111258800-111260200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr3:111258800-111260200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr3:111258800-111260200	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr3:111258800-111260200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:111258800-111260400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:111258800-111260400	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr3:111258800-111260400	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr3:111258800-111260400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr3:111258800-111260400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr3:111258800-111260400	Weak transcription	Fetal Lung	lung
30	chr3:111258800-111260800	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr3:111258800-111260800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr3:111258800-111261000	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr3:111258800-111264200	Weak transcription	Stomach Mucosa	stomach
34	chr3:111258800-111266600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:111259000-111259600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr3:111259000-111260000	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr3:111259000-111260200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:111259000-111260200	Enhancers	Dnd41	blood
39	chr3:111259000-111260800	Weak transcription	Duodenum Mucosa	Duodenum
40	chr3:111259000-111264000	Weak transcription	Fetal Intestine Small	intestine

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