Variant report

Variant	rs1248861
Chromosome Location	chr3:85008048-85008049
allele	A/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	SP1	chr3:85007685-85008189	HepG2	liver:	n/a	chr3:85008037-85008047 chr3:85008091-85008101 chr3:85007803-85007813 chr3:85008090-85008102 chr3:85008036-85008048 chr3:85007803-85007813 chr3:85008090-85008102 chr3:85008038-85008047 chr3:85008092-85008101 chr3:85007803-85007817 chr3:85007803-85007812 chr3:85007812-85007833 chr3:85008092-85008101 chr3:85007802-85007814 chr3:85008091-85008100 chr3:85008064-85008073 chr3:85008062-85008074 chr3:85008037-85008046 chr3:85008087-85008101 chr3:85007802-85007814 chr3:85008091-85008101 chr3:85007804-85007813 chr3:85008010-85008031 chr3:85007803-85007812 chr3:85007953-85007966
2	PBX3	chr3:85007914-85008164	GM12878	blood:	n/a	chr3:85008020-85008029
3	MAX	chr3:85007951-85008480	K562	blood:	n/a	chr3:85008089-85008099 chr3:85008037-85008047
4	NFYA	chr3:85007657-85008295	K562	blood:	n/a	chr3:85008050-85008064 chr3:85008018-85008032 chr3:85007819-85007834 chr3:85008020-85008030 chr3:85007823-85007835 chr3:85008017-85008032 chr3:85008017-85008032 chr3:85007819-85007834
5	CREB1	chr3:85007924-85008243	A549	lung:	n/a	n/a
6	SP4	chr3:85007578-85008193	H1-hESC	embryonic stem cell:	n/a	chr3:85007802-85007818 chr3:85008088-85008104 chr3:85008086-85008102 chr3:85007800-85007816 chr3:85008058-85008074
7	MAX	chr3:85007487-85008599	ECC-1	luminal epithelium:	n/a	chr3:85008089-85008099 chr3:85008037-85008047 chr3:85007805-85007815
8	MAX	chr3:85007409-85008751	A549	lung:	n/a	chr3:85008089-85008099 chr3:85008037-85008047 chr3:85007805-85007815
9	TAF1	chr3:85007638-85008549	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr3:85007453-85008645	ECC-1	luminal epithelium:	n/a	chr3:85008089-85008099 chr3:85008037-85008047 chr3:85007805-85007815
11	CHD2	chr3:85007823-85008268	GM12878	blood:	n/a	n/a
12	SP1	chr3:85007498-85009254	H1-hESC	embryonic stem cell:	n/a	chr3:85008037-85008047 chr3:85008091-85008101 chr3:85008933-85008945 chr3:85007803-85007813 chr3:85008934-85008948 chr3:85008090-85008102 chr3:85008933-85008945 chr3:85008036-85008048 chr3:85007803-85007813 chr3:85008823-85008835 chr3:85008935-85008944 chr3:85008824-85008833 chr3:85008090-85008102 chr3:85008038-85008047 chr3:85007624-85007634 chr3:85008824-85008833 chr3:85008092-85008101 chr3:85007803-85007817 chr3:85007803-85007812 chr3:85007812-85007833 chr3:85008092-85008101 chr3:85007802-85007814 chr3:85008091-85008100 chr3:85008064-85008073 chr3:85008062-85008074 chr3:85008037-85008046 chr3:85008087-85008101 chr3:85007802-85007814 chr3:85008825-85008834 chr3:85008091-85008101 chr3:85007804-85007813 chr3:85008010-85008031 chr3:85007803-85007812 chr3:85007953-85007966
13	NFYB	chr3:85007624-85008354	K562	blood:	n/a	chr3:85008050-85008064 chr3:85008018-85008032 chr3:85007819-85007834 chr3:85008020-85008030 chr3:85007823-85007835 chr3:85008017-85008032 chr3:85008017-85008032 chr3:85007819-85007834 chr3:85007821-85007836
14	POLR2A	chr3:85007683-85009152	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr3:85007333-85008819	H1-hESC	embryonic stem cell:	n/a	n/a
16	E2F4	chr3:85007670-85008193	MCF10A-Er-Src	breast:	n/a	chr3:85007804-85007813 chr3:85008091-85008100 chr3:85007823-85007832
17	MAX	chr3:85007591-85008616	MCF-7	breast:	n/a	chr3:85008089-85008099 chr3:85008037-85008047 chr3:85007805-85007815
18	MXI1	chr3:85007415-85011781	SK-N-SH	brain:	n/a	n/a
19	SP4	chr3:85007686-85008048	H1-hESC	embryonic stem cell:	n/a	chr3:85007802-85007818 chr3:85007800-85007816
20	E2F6	chr3:85007456-85008625	A549	lung:	n/a	chr3:85007804-85007813 chr3:85008091-85008100 chr3:85007823-85007832
21	RCOR1	chr3:85007848-85008434	HepG2	liver:	n/a	n/a
22	YY1	chr3:85007956-85008390	HepG2	liver:	n/a	chr3:85008088-85008102 chr3:85008091-85008100
23	EP300	chr3:85007861-85008518	ECC-1	luminal epithelium:	n/a	n/a
24	SP2	chr3:85007818-85008060	K562	blood:	n/a	chr3:85008019-85008029
25	IRF1	chr3:85007754-85008173	K562	blood:	n/a	chr3:85007823-85007832 chr3:85008062-85008076 chr3:85008090-85008104 chr3:85007800-85007814
26	E2F4	chr3:85007835-85008114	GM12878	blood:	n/a	chr3:85008091-85008100
27	EGR1	chr3:85007944-85008129	K562	blood:	n/a	chr3:85008086-85008099 chr3:85008091-85008101 chr3:85008036-85008046 chr3:85008089-85008099
28	POLR2A	chr3:85007722-85009541	H1-neurons	neurons:	n/a	n/a
29	POLR2A	chr3:85007675-85008491	MCF-7	breast:	n/a	n/a
30	NFYB	chr3:85007611-85008077	Hela-S3	cervix:	n/a	chr3:85008050-85008064 chr3:85008018-85008032 chr3:85007819-85007834 chr3:85008020-85008030 chr3:85007823-85007835 chr3:85008017-85008032 chr3:85008017-85008032 chr3:85007819-85007834 chr3:85007821-85007836
31	FOXA2	chr3:85007811-85008051	HepG2	liver:	n/a	n/a
32	NFYA	chr3:85007636-85008296	Hela-S3	cervix:	n/a	chr3:85008050-85008064 chr3:85008018-85008032 chr3:85007819-85007834 chr3:85008020-85008030 chr3:85007823-85007835 chr3:85008017-85008032 chr3:85008017-85008032 chr3:85007819-85007834
33	SP1	chr3:85007633-85008228	GM12878	blood:	n/a	chr3:85008037-85008047 chr3:85008091-85008101 chr3:85007803-85007813 chr3:85008090-85008102 chr3:85008036-85008048 chr3:85007803-85007813 chr3:85008090-85008102 chr3:85008038-85008047 chr3:85008092-85008101 chr3:85007803-85007817 chr3:85007803-85007812 chr3:85007812-85007833 chr3:85008092-85008101 chr3:85007802-85007814 chr3:85008091-85008100 chr3:85008064-85008073 chr3:85008062-85008074 chr3:85008037-85008046 chr3:85008087-85008101 chr3:85007802-85007814 chr3:85008091-85008101 chr3:85007804-85007813 chr3:85008010-85008031 chr3:85007803-85007812 chr3:85007953-85007966
34	SP1	chr3:85007525-85008176	H1-hESC	embryonic stem cell:	n/a	chr3:85008037-85008047 chr3:85008091-85008101 chr3:85007803-85007813 chr3:85008090-85008102 chr3:85008036-85008048 chr3:85007803-85007813 chr3:85008090-85008102 chr3:85008038-85008047 chr3:85007624-85007634 chr3:85008092-85008101 chr3:85007803-85007817 chr3:85007803-85007812 chr3:85007812-85007833 chr3:85008092-85008101 chr3:85007802-85007814 chr3:85008091-85008100 chr3:85008064-85008073 chr3:85008062-85008074 chr3:85008037-85008046 chr3:85008087-85008101 chr3:85007802-85007814 chr3:85008091-85008101 chr3:85007804-85007813 chr3:85008010-85008031 chr3:85007803-85007812 chr3:85007953-85007966
35	POLR2A	chr3:85007681-85008676	H1-neurons	neurons:	n/a	n/a
36	E2F6	chr3:85007992-85008249	K562	blood:	n/a	chr3:85008091-85008100
37	CHD2	chr3:85007616-85008518	H1-hESC	embryonic stem cell:	n/a	n/a
38	FOXA1	chr3:85007796-85008200	HepG2	liver:	n/a	n/a
39	SIN3A	chr3:85007498-85011149	H1-hESC	embryonic stem cell:	n/a	chr3:85008956-85008967 chr3:85007753-85007766
40	TAF1	chr3:85007505-85009261	H1-hESC	embryonic stem cell:	n/a	n/a
41	FOXA2	chr3:85007671-85008321	A549	lung:	n/a	n/a
42	TAF1	chr3:85007917-85008360	ECC-1	luminal epithelium:	n/a	n/a
43	E2F6	chr3:85007596-85008710	H1-hESC	embryonic stem cell:	n/a	chr3:85007804-85007813 chr3:85008091-85008100 chr3:85007823-85007832
44	MAX	chr3:85007564-85008606	HepG2	liver:	n/a	chr3:85008089-85008099 chr3:85008037-85008047 chr3:85007805-85007815
45	MAX	chr3:85007557-85008672	SK-N-SH	brain:	n/a	chr3:85008089-85008099 chr3:85008037-85008047 chr3:85007805-85007815
46	MAX	chr3:85007536-85008608	A549	lung:	n/a	chr3:85008089-85008099 chr3:85008037-85008047 chr3:85007805-85007815
47	CHD2	chr3:85007816-85008169	HepG2	liver:	n/a	n/a
48	RFX5	chr3:85007862-85008055	Hela-S3	cervix:	n/a	chr3:85008020-85008029
49	E2F6	chr3:85007957-85008343	A549	lung:	n/a	chr3:85008091-85008100
50	FOXA1	chr3:85007817-85008060	T-47D	breast:	n/a	n/a

Variant related genes	Relation type
CADM2	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1248858	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1248859	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13081745	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1694977	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1872556	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2035561	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2035562	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2326123	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4569672	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs653481	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs765461	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3381298	chr3:84689266-85030314	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1002058	chr3:84757044-85389876	Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1001316	chr3:84773522-85071342	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv877091	chr3:84876250-85069287	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv482371	chr3:84880813-85031486	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv471620	chr3:84880814-85031486	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv1829788	chr3:84926769-85086403	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1010140	chr3:84997012-85034281	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:85007200-85008800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
2	chr3:85007200-85009600	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr3:85007200-85011800	Active TSS	H1 Cell Line	embryonic stem cell
4	chr3:85007200-85012400	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr3:85007200-85012600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:85007400-85008200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr3:85007400-85008200	Bivalent/Poised TSS	Primary hematopoietic stem cells short term culture	blood
8	chr3:85007400-85008200	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr3:85007400-85008200	Active TSS	Stomach Smooth Muscle	stomach
10	chr3:85007400-85008400	Active TSS	Brain Germinal Matrix	brain
11	chr3:85007400-85008600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr3:85007400-85008800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:85007400-85008800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:85007400-85008800	Active TSS	NH-A	brain
15	chr3:85007400-85009200	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr3:85007400-85009200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:85007400-85009600	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr3:85007400-85009800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr3:85007400-85009800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:85007400-85011200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr3:85007400-85011600	Active TSS	H9 Cell Line	embryonic stem cell
22	chr3:85007400-85012000	Active TSS	Brain Cingulate Gyrus	brain
23	chr3:85007600-85008200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:85007600-85008200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:85007600-85008200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr3:85007600-85008200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr3:85007600-85008200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:85007600-85008200	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:85007600-85008200	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:85007600-85008200	Active TSS	Colonic Mucosa	Colon
31	chr3:85007600-85008200	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
32	chr3:85007600-85008200	Active TSS	Gastric	stomach
33	chr3:85007600-85008200	Enhancers	Left Ventricle	heart
34	chr3:85007600-85008200	Active TSS	Rectal Mucosa Donor 31	rectum
35	chr3:85007600-85008200	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
36	chr3:85007600-85008200	Active TSS	GM12878-XiMat	blood
37	chr3:85007600-85008200	Active TSS	HMEC	breast
38	chr3:85007600-85008200	Active TSS	HUVEC	blood vessel
39	chr3:85007600-85008200	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
40	chr3:85007600-85008200	Active TSS	Osteobl	bone
41	chr3:85007600-85008400	Active TSS	Primary T helper naive cells from peripheral blood	blood
42	chr3:85007600-85008400	Active TSS	K562	blood
43	chr3:85007600-85008600	Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr3:85007600-85008600	Bivalent/Poised TSS	Fetal Kidney	kidney
45	chr3:85007600-85008600	Bivalent/Poised TSS	Thymus	Thymus
46	chr3:85007600-85008600	Active TSS	A549	lung
47	chr3:85007600-85008600	Active TSS	Hela-S3	cervix
48	chr3:85007600-85008600	Active TSS	HSMMtube	muscle
49	chr3:85007600-85008600	Active TSS	NHEK	skin
50	chr3:85007600-85008600	Active TSS	NHLF	lung

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