Variant report

Variant	rs348938
Chromosome Location	chr5:112825032-112825033
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	SETDB1	chr5:112824923-112825401	U2OS	brain:	n/a	n/a
2	EP300	chr5:112825014-112825435	SK-N-SH_RA	brain:	n/a	chr5:112825226-112825235 chr5:112825227-112825236
3	FOS	chr5:112824950-112825432	HUVEC	blood vessel:	n/a	chr5:112825227-112825235 chr5:112825227-112825234 chr5:112825226-112825235 chr5:112825225-112825236 chr5:112825226-112825236
4	NFIC	chr5:112825024-112825393	GM12878	blood:	n/a	n/a
5	POLR2A	chr5:112824960-112825488	SK-N-SH	brain:	n/a	n/a
6	TEAD4	chr5:112825017-112825580	SK-N-SH	brain:	n/a	n/a
7	FOSL2	chr5:112825014-112825560	SK-N-SH	brain:	n/a	chr5:112825227-112825235 chr5:112825227-112825234 chr5:112825226-112825235 chr5:112825226-112825236
8	JUND	chr5:112824784-112825647	HCT-116	colon:	n/a	chr5:112825227-112825235 chr5:112825225-112825236 chr5:112825227-112825234 chr5:112825226-112825235 chr5:112825226-112825236
9	MYC	chr5:112824005-112825442	MCF10A-Er-Src	breast:	n/a	chr5:112825226-112825235 chr5:112825227-112825236
10	STAT3	chr5:112825017-112825396	MCF10A-Er-Src	breast:	n/a	chr5:112825226-112825235 chr5:112825227-112825236
11	SP1	chr5:112824888-112825620	HCT-116	colon:	n/a	n/a
12	YY1	chr5:112825016-112825398	SK-N-SH_RA	brain:	n/a	n/a
13	MAX	chr5:112824869-112825529	SK-N-SH	brain:	n/a	chr5:112825226-112825235 chr5:112825227-112825236
14	FOS	chr5:112824953-112825510	MCF10A-Er-Src	breast:	n/a	chr5:112825227-112825235 chr5:112825227-112825234 chr5:112825226-112825235 chr5:112825225-112825236 chr5:112825226-112825236
15	CBX3	chr5:112824784-112825698	HCT-116	colon:	n/a	n/a
16	JUN	chr5:112824963-112825407	Hela-S3	cervix:	n/a	chr5:112825227-112825235 chr5:112825227-112825234 chr5:112825226-112825235 chr5:112825226-112825236
17	FOSL1	chr5:112824934-112825697	HCT-116	colon:	n/a	chr5:112825227-112825235 chr5:112825227-112825234 chr5:112825226-112825235 chr5:112825226-112825236
18	STAT3	chr5:112824981-112825433	MCF10A-Er-Src	breast:	n/a	chr5:112825226-112825235 chr5:112825227-112825236
19	MYC	chr5:112825027-112825428	NB4	blood:	n/a	chr5:112825226-112825235 chr5:112825227-112825236
20	FOSL2	chr5:112824948-112825456	A549	lung:	n/a	chr5:112825227-112825235 chr5:112825227-112825234 chr5:112825226-112825235 chr5:112825226-112825236
21	GATA3	chr5:112824770-112825588	SK-N-SH	brain:	n/a	chr5:112825225-112825234
22	CEBPB	chr5:112824567-112825739	HCT-116	colon:	n/a	n/a
23	MAX	chr5:112823020-112825593	HCT-116	colon:	n/a	chr5:112823284-112823295 chr5:112825226-112825235 chr5:112825227-112825236
24	TCF12	chr5:112824885-112825690	SK-N-SH	brain:	n/a	n/a
25	PBX3	chr5:112824919-112825529	SK-N-SH	brain:	n/a	n/a
26	PBX3	chr5:112824917-112825533	SK-N-SH	brain:	n/a	n/a
27	JUND	chr5:112823928-112825693	SK-N-SH	brain:	n/a	chr5:112825227-112825235 chr5:112825225-112825236 chr5:112825227-112825234 chr5:112825226-112825235 chr5:112825226-112825236 chr5:112824634-112824643
28	SP1	chr5:112824749-112825647	HCT-116	colon:	n/a	n/a
29	JUND	chr5:112824881-112825591	SK-N-SH	brain:	n/a	chr5:112825227-112825235 chr5:112825225-112825236 chr5:112825227-112825234 chr5:112825226-112825235 chr5:112825226-112825236
30	JUND	chr5:112824912-112825620	SK-N-SH	brain:	n/a	chr5:112825227-112825235 chr5:112825225-112825236 chr5:112825227-112825234 chr5:112825226-112825235 chr5:112825226-112825236
31	YY1	chr5:112824957-112825444	SK-N-SH	brain:	n/a	n/a
32	JUND	chr5:112823904-112825645	HCT-116	colon:	n/a	chr5:112825227-112825235 chr5:112825225-112825236 chr5:112825227-112825234 chr5:112825226-112825235 chr5:112825226-112825236 chr5:112824634-112824643
33	RUNX3	chr5:112824932-112825444	GM12878	blood:	n/a	chr5:112825212-112825221 chr5:112825212-112825221
34	MAX	chr5:112824877-112825545	SK-N-SH	brain:	n/a	chr5:112825226-112825235 chr5:112825227-112825236
35	POLR2A	chr5:112823537-112825448	IMR90	lung:	n/a	n/a
36	POLR2A	chr5:112824969-112825408	U87	brain:	n/a	n/a
37	FOS	chr5:112824962-112825506	MCF10A-Er-Src	breast:	n/a	chr5:112825227-112825235 chr5:112825227-112825234 chr5:112825226-112825235 chr5:112825225-112825236 chr5:112825226-112825236
38	EP300	chr5:112824976-112825365	SK-N-SH_RA	brain:	n/a	chr5:112825226-112825235 chr5:112825227-112825236
39	GATA3	chr5:112824853-112825613	SK-N-SH	brain:	n/a	chr5:112825225-112825234
40	FOSL1	chr5:112823968-112825681	HCT-116	colon:	n/a	chr5:112825227-112825235 chr5:112825227-112825234 chr5:112825226-112825235 chr5:112825226-112825236 chr5:112824634-112824643
41	RUNX3	chr5:112824996-112825399	GM12878	blood:	n/a	chr5:112825212-112825221 chr5:112825212-112825221
42	REST	chr5:112824988-112825280	SK-N-SH	brain:	n/a	n/a
43	TEAD4	chr5:112824954-112825542	SK-N-SH	brain:	n/a	n/a
44	E2F4	chr5:112824987-112825484	MCF10A-Er-Src	breast:	n/a	n/a
45	FOS	chr5:112824914-112825510	MCF10A-Er-Src	breast:	n/a	chr5:112825227-112825235 chr5:112825227-112825234 chr5:112825226-112825235 chr5:112825225-112825236 chr5:112825226-112825236
46	MYC	chr5:112824948-112825410	MCF10A-Er-Src	breast:	n/a	chr5:112825226-112825235 chr5:112825227-112825236
47	TCF12	chr5:112824829-112825649	SK-N-SH	brain:	n/a	n/a
48	RCOR1	chr5:112824988-112825317	Hela-S3	cervix:	n/a	n/a
49	CEBPB	chr5:112825025-112825387	HepG2	liver:	n/a	n/a
50	CEBPB	chr5:112825010-112825691	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112823438..112825437-chr5:112848716..112850682,3	MCF-7	breast:
2	chr5:112823064..112825616-chr5:112827873..112829693,2	MCF-7	breast:

Variant related genes	Relation type
RNU4ATAC13P	TF binding region
MCC	TF binding region
ENSG00000251741	Chromatin interaction
ENSG00000047188	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10040430	0.85[AFR][1000 genomes]
rs10046057	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs1057827	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs11241210	0.85[AFR][1000 genomes]
rs168365	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs168366	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs171180	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs191553	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2248930	0.81[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs26991	0.89[YRI][hapmap]
rs28848005	0.85[AFR][1000 genomes]
rs3097242	0.80[AFR][1000 genomes]
rs348924	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs348925	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs348926	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs348928	0.81[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs348929	0.82[CEU][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs348930	0.82[CEU][hapmap];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs348931	0.82[CEU][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs348932	0.82[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs348940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs348941	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs348944	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs348945	0.82[AFR][1000 genomes]
rs348946	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs348947	0.82[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs348948	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs348951	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs348952	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs348954	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs348955	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs348956	0.82[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs348957	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs348958	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs348960	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs348961	0.81[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs348962	0.81[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs348963	0.81[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs364738	0.82[CEU][hapmap];0.96[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs366219	0.89[AFR][1000 genomes]
rs367943	0.81[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs3842917	1.00[YRI][hapmap]
rs388363	0.96[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs444322	0.82[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs451425	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs451453	0.88[AFR][1000 genomes]
rs455435	0.82[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs458044	0.86[AFR][1000 genomes]
rs460079	0.82[CEU][hapmap]
rs463167	0.82[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs463249	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs4705821	1.00[YRI][hapmap]
rs4705823	1.00[YRI][hapmap]
rs4705827	0.82[YRI][hapmap]
rs644154	0.82[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs6594718	0.96[YRI][hapmap]
rs6594721	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs6594732	0.82[YRI][hapmap]
rs6594733	0.82[YRI][hapmap]
rs6876448	0.81[AFR][1000 genomes]
rs6880447	0.85[AFR][1000 genomes]
rs6887816	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs7709110	1.00[YRI][hapmap]
rs7730801	0.96[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112822800-112825200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
2	chr5:112823000-112825200	Active TSS	Aorta	Aorta
3	chr5:112823200-112825200	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr5:112823400-112825400	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
5	chr5:112823400-112825600	Active TSS	Brain Anterior Caudate	brain
6	chr5:112823800-112825600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr5:112823800-112826800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
8	chr5:112824000-112825400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
9	chr5:112824200-112825200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr5:112824200-112825200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
11	chr5:112824200-112825600	Flanking Active TSS	NH-A	brain
12	chr5:112824400-112825200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr5:112824400-112825200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr5:112824400-112825200	Flanking Active TSS	HSMM	muscle
15	chr5:112824400-112825200	Flanking Active TSS	HSMMtube	muscle
16	chr5:112824400-112825200	Flanking Active TSS	Osteobl	bone
17	chr5:112824400-112825600	Bivalent Enhancer	Stomach Mucosa	stomach
18	chr5:112824400-112825800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr5:112824400-112825800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
20	chr5:112824600-112825200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
21	chr5:112824600-112825200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr5:112824600-112825200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
23	chr5:112824600-112825200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
24	chr5:112824600-112825200	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr5:112824600-112825200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr5:112824600-112825200	Flanking Active TSS	NHDF-Ad	bronchial
27	chr5:112824600-112825400	Bivalent Enhancer	Small Intestine	intestine
28	chr5:112824600-112825600	Enhancers	Esophagus	oesophagus
29	chr5:112824600-112825600	Enhancers	Hela-S3	cervix
30	chr5:112824600-112825800	Enhancers	Placenta Amnion	Placenta Amnion
31	chr5:112824600-112826000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr5:112824600-112826000	Enhancers	Dnd41	blood
33	chr5:112824800-112825200	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
34	chr5:112824800-112825200	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
35	chr5:112824800-112825200	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
36	chr5:112824800-112825200	Bivalent Enhancer	Adipose Nuclei	Adipose
37	chr5:112824800-112825200	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr5:112824800-112825200	Enhancers	Colon Smooth Muscle	Colon
39	chr5:112824800-112825200	Bivalent Enhancer	Duodenum Mucosa	Duodenum
40	chr5:112824800-112825200	Bivalent Enhancer	Fetal Intestine Small	intestine
41	chr5:112824800-112825200	Bivalent Enhancer	Placenta	Placenta
42	chr5:112824800-112825400	Enhancers	Brain Cingulate Gyrus	brain
43	chr5:112824800-112825600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
44	chr5:112824800-112825600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr5:112824800-112825600	Enhancers	HUVEC	blood vessel
46	chr5:112824800-112825800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr5:112824800-112826000	Enhancers	NHLF	lung
48	chr5:112825000-112825200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr5:112825000-112825200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
50	chr5:112825000-112825200	Enhancers	Brain Hippocampus Middle	brain

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