Variant report

Variant	rs348940
Chromosome Location	chr5:112824530-112824531
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	SIN3A	chr5:112823093-112824677	H1-hESC	embryonic stem cell:	n/a	n/a
2	TAF1	chr5:112823922-112824538	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr5:112823907-112824587	SK-N-MC	brain:	n/a	n/a
4	YY1	chr5:112823303-112824699	SK-N-SH	brain:	n/a	n/a
5	FOXA1	chr5:112824101-112824833	T-47D	breast:	n/a	n/a
6	HDAC2	chr5:112823117-112824812	MCF-7	breast:	n/a	chr5:112823289-112823308
7	EP300	chr5:112823670-112824570	SK-N-SH	brain:	n/a	n/a
8	YY1	chr5:112823839-112824686	SK-N-SH_RA	brain:	n/a	n/a
9	E2F6	chr5:112823135-112824738	H1-hESC	embryonic stem cell:	n/a	chr5:112823823-112823830 chr5:112823822-112823834 chr5:112823252-112823261 chr5:112823881-112823895 chr5:112823823-112823830 chr5:112823823-112823830
10	MAX	chr5:112823346-112824833	MCF-7	breast:	n/a	n/a
11	POLR2A	chr5:112822969-112824751	H1-hESC	embryonic stem cell:	n/a	n/a
12	TAF1	chr5:112823874-112824535	H1-neurons	neurons:	n/a	n/a
13	NRF1	chr5:112823874-112824880	SK-N-SH	brain:	n/a	chr5:112823887-112823896
14	MYC	chr5:112824005-112825442	MCF10A-Er-Src	breast:	n/a	chr5:112825226-112825235 chr5:112825227-112825236
15	MAX	chr5:112823544-112824602	A549	lung:	n/a	n/a
16	POLR2A	chr5:112823476-112824647	MCF-7	breast:	n/a	n/a
17	POLR2A	chr5:112823844-112824787	MCF-7	breast:	n/a	n/a
18	MAX	chr5:112823020-112825593	HCT-116	colon:	n/a	chr5:112823284-112823295 chr5:112825226-112825235 chr5:112825227-112825236
19	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
20	TAF1	chr5:112823117-112824574	H1-hESC	embryonic stem cell:	n/a	n/a
21	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
22	POLR2A	chr5:112823971-112824540	ECC-1	luminal epithelium:	n/a	n/a
23	NR2F2	chr5:112823569-112824569	MCF-7	breast:	n/a	n/a
24	POLR2A	chr5:112823537-112825448	IMR90	lung:	n/a	n/a
25	YY1	chr5:112823931-112824725	SK-N-SH	brain:	n/a	n/a
26	TEAD4	chr5:112823553-112824566	SK-N-SH	brain:	n/a	n/a
27	POLR2A	chr5:112824057-112824533	H1-hESC	embryonic stem cell:	n/a	n/a
28	MAX	chr5:112823437-112824570	H1-hESC	embryonic stem cell:	n/a	n/a
29	FOSL1	chr5:112823968-112825681	HCT-116	colon:	n/a	chr5:112825227-112825235 chr5:112825227-112825234 chr5:112825226-112825235 chr5:112825226-112825236 chr5:112824634-112824643
30	HA-E2F1	chr5:112822998-112824828	MCF-7	breast:	n/a	chr5:112823823-112823830 chr5:112823822-112823834 chr5:112823252-112823261 chr5:112823881-112823895 chr5:112823823-112823830 chr5:112823823-112823830 chr5:112823028-112823037
31	POLR2A	chr5:112823870-112824562	H1-neurons	neurons:	n/a	n/a
32	REST	chr5:112823624-112824953	H1-neurons	neurons:	n/a	chr5:112823714-112823721
33	CTBP2	chr5:112823154-112824556	H1-hESC	embryonic stem cell:	n/a	n/a
34	GTF2F1	chr5:112824092-112824643	H1-hESC	embryonic stem cell:	n/a	n/a
35	YY1	chr5:112823470-112824702	SK-N-SH_RA	brain:	n/a	n/a
36	MAX	chr5:112823651-112824589	ECC-1	luminal epithelium:	n/a	n/a
37	STAT3	chr5:112824251-112824635	MCF10A-Er-Src	breast:	n/a	n/a
38	POLR2A	chr5:112823205-112824740	H1-hESC	embryonic stem cell:	n/a	n/a
39	ZNF263	chr5:112823060-112825316	HEK293-T-REx	kidney:	n/a	chr5:112824318-112824339
40	POLR2A	chr5:112823189-112824731	MCF-7	breast:	n/a	n/a
41	CREB1	chr5:112823715-112824553	H1-hESC	embryonic stem cell:	n/a	n/a
42	KAP1	chr5:112823836-112825464	HEK293	kidney:	n/a	chr5:112825228-112825237
43	YY1	chr5:112823907-112824637	H1-hESC	embryonic stem cell:	n/a	n/a
44	EP300	chr5:112823799-112824550	ECC-1	luminal epithelium:	n/a	n/a
45	RAD21	chr5:112823780-112824533	H1-hESC	embryonic stem cell:	n/a	n/a
46	MAX	chr5:112823314-112824562	H1-hESC	embryonic stem cell:	n/a	n/a
47	ELF1	chr5:112823920-112824631	MCF-7	breast:	n/a	n/a
48	RCOR1	chr5:112822825-112826281	IMR90	lung:	n/a	n/a
49	MAZ	chr5:112823544-112826068	IMR90	lung:	n/a	chr5:112825226-112825235 chr5:112825227-112825236
50	POLR2A	chr5:112823905-112825506	MCF10A-Er-Src	breast:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:112824497-112824547	HMEC	breast:	n/a
2	chr5:112824497-112824547	HEK293	kidney:	embryo
3	chr5:112824497-112824547	GM06990	blood:	n/a
4	chr5:112824497-112824547	RPTEC	kidney:	n/a
5	chr5:112824497-112824547	T-47D	breast:	n/a
6	chr5:112824497-112824547	K562	blood:	n/a
7	chr5:112824497-112824547	BE2_C	brain:	n/a
8	chr5:112824497-112824547	HRCEpiC	kidney:	n/a
9	chr5:112824497-112824547	PrEC	prostate:	n/a
10	chr5:112824497-112824547	HPAEpiC	pulmonary alveolar:	n/a
11	chr5:112824497-112824547	CMK	blood:	n/a
12	chr5:112824497-112824547	PFSK-1	brain:	n/a
13	chr5:112824497-112824547	GM12892	blood:	n/a
14	chr5:112824497-112824547	A549	lung:	n/a
15	chr5:112824497-112824547	PANC-1	pancreas:	n/a
16	chr5:112824497-112824547	Hela-S3	cervix:	n/a
17	chr5:112824497-112824547	LNCaP	prostate:	n/a
18	chr5:112824497-112824547	AG04449	skin:	fetal
19	chr5:112824497-112824547	HepG2	liver:	n/a
20	chr5:112824497-112824547	BJ	skin:	n/a
21	chr5:112824497-112824547	MCF10A-Er-Src	breast:	n/a
22	chr5:112824497-112824547	U87	brain:	n/a
23	chr5:112824497-112824547	ECC-1	luminal epithelium:	n/a
24	chr5:112824497-112824547	HL-60	blood:	n/a
25	chr5:112824497-112824547	GM12891	blood:	n/a
26	chr5:112824497-112824547	HAEpiC	amniotic membrane:	n/a
27	chr5:112824497-112824547	Jurkat	blood:	n/a
28	chr5:112824497-112824547	AG09309	skin:	n/a
29	chr5:112824497-112824547	NT2-D1	testis:	n/a
30	chr5:112824497-112824547	AG09319	gingival:	n/a
31	chr5:112824497-112824547	NH-A	brain:	n/a
32	chr5:112824497-112824547	GM19239	blood:	n/a
33	chr5:112824497-112824547	HCF	heart:	n/a
34	chr5:112824497-112824547	SK-N-SH_RA	brain:	n/a
35	chr5:112824497-112824547	GM12878	blood:	n/a
36	chr5:112824497-112824547	AoSMC	blood vessel:	n/a
37	chr5:112824497-112824547	HNPCEpiC	eye:	n/a
38	chr5:112824497-112824547	SK-N-MC	brain:	n/a
39	chr5:112824497-112824547	NHBE	bronchial:	n/a
40	chr5:112824497-112824547	NB4	blood:	n/a
41	chr5:112824497-112824547	IMR90	lung:	fetal
42	chr5:112824497-112824547	MCF-7	breast:	n/a
43	chr5:112824497-112824547	HRPEpiC	eye:	n/a
44	chr5:112824497-112824547	HEEpiC	esophagus:	n/a
45	chr5:112824497-112824547	HCT-116	colon:	n/a
46	chr5:112824497-112824547	NHDF-neo	bronchial:	n/a
47	chr5:112824497-112824547	ovcar-3	ovarian:	n/a
48	chr5:112824497-112824547	HCM	heart:	n/a
49	chr5:112824497-112824547	ProgFib	skin:	n/a
50	chr5:112824497-112824547	Caco-2	colon:	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
MCC	TF binding region
MCC	CpG island
ENSG00000251741	Chromatin interaction
ENSG00000047188	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10040430	0.85[AFR][1000 genomes]
rs10046057	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	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes]
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	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs348929	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs348930	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs348931	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs348932	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs348938	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	0.97[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	0.98[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	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs348962	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs348963	0.97[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs364738	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs366219	0.89[AFR][1000 genomes]
rs367943	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs388363	0.96[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs444322	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	0.86[AFR][1000 genomes]
rs458044	0.86[AFR][1000 genomes]
rs463167	0.86[AFR][1000 genomes]
rs463249	0.83[AFR][1000 genomes]
rs644154	0.86[AFR][1000 genomes]
rs6594721	0.81[AFR][1000 genomes]
rs6876448	0.81[AFR][1000 genomes]
rs6880447	0.85[AFR][1000 genomes]
rs6887816	0.85[AFR][1000 genomes]

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:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112822200-112824600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:112822600-112824600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:112822800-112824600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr5:112822800-112824800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
5	chr5:112822800-112825000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
6	chr5:112822800-112825200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
7	chr5:112823000-112824600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr5:112823000-112824600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr5:112823000-112824600	Active TSS	Ovary	ovary
10	chr5:112823000-112824600	Active TSS	NHLF	lung
11	chr5:112823000-112824800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr5:112823000-112824800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
13	chr5:112823000-112825000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
14	chr5:112823000-112825000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
15	chr5:112823000-112825000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
16	chr5:112823000-112825000	Active TSS	Fetal Kidney	kidney
17	chr5:112823000-112825000	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr5:112823000-112825200	Active TSS	Aorta	Aorta
19	chr5:112823200-112824600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
20	chr5:112823200-112824600	Active TSS	Fetal Heart	heart
21	chr5:112823200-112824600	Active TSS	Left Ventricle	heart
22	chr5:112823200-112824600	Bivalent/Poised TSS	Thymus	Thymus
23	chr5:112823200-112824800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
24	chr5:112823200-112824800	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
25	chr5:112823200-112825200	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr5:112823400-112824600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr5:112823400-112824600	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
28	chr5:112823400-112824600	Flanking Bivalent TSS/Enh	Lung	lung
29	chr5:112823400-112824800	Active TSS	H9 Cell Line	embryonic stem cell
30	chr5:112823400-112824800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
31	chr5:112823400-112824800	Active TSS	Brain Substantia Nigra	brain
32	chr5:112823400-112824800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
33	chr5:112823400-112825000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
34	chr5:112823400-112825000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
35	chr5:112823400-112825400	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
36	chr5:112823400-112825600	Active TSS	Brain Anterior Caudate	brain
37	chr5:112823600-112824600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr5:112823600-112824600	Active TSS	Esophagus	oesophagus
39	chr5:112823600-112824600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
40	chr5:112823600-112824600	Active TSS	NHDF-Ad	bronchial
41	chr5:112823600-112824800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr5:112823600-112825000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr5:112823800-112824600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr5:112823800-112824600	Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr5:112823800-112824600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr5:112823800-112824600	Active TSS	Brain Cingulate Gyrus	brain
47	chr5:112823800-112824600	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr5:112823800-112824600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr5:112823800-112824600	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
50	chr5:112823800-112824600	Bivalent/Poised TSS	Fetal Brain Female	brain

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