Variant report

Variant	rs4855875
Chromosome Location	chr3:49448659-49448660
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	MXI1	chr3:49448142-49450226	GM12878	blood:	n/a	n/a
2	WRNIP1	chr3:49448480-49448988	GM12878	blood:	n/a	n/a
3	MAX	chr3:49448496-49450106	Hela-S3	cervix:	n/a	chr3:49448867-49448876 chr3:49448924-49448934 chr3:49449585-49449594
4	MAZ	chr3:49448615-49450630	IMR90	lung:	n/a	chr3:49450267-49450276 chr3:49448867-49448876 chr3:49448924-49448934 chr3:49449585-49449594
5	CUX1	chr3:49448301-49448829	K562	blood:	n/a	chr3:49448775-49448784 chr3:49448496-49448505
6	TAF1	chr3:49448591-49450306	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr3:49448355-49448755	HUVEC	blood vessel:	n/a	n/a
8	HCFC1	chr3:49448164-49450849	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr3:49448595-49451034	HUVEC	blood vessel:	n/a	n/a
10	CUX1	chr3:49448127-49448665	GM12878	blood:	n/a	chr3:49448496-49448505
11	TCF12	chr3:49448649-49450220	ECC-1	luminal epithelium:	n/a	n/a
12	CHD1	chr3:49448648-49450470	GM12878	blood:	n/a	n/a
13	POLR2A	chr3:49448292-49450804	IMR90	lung:	n/a	n/a
14	POLR2A	chr3:49448395-49450585	PBDE	blood:	n/a	n/a
15	CHD1	chr3:49446752-49450840	IMR90	lung:	n/a	n/a
16	POLR2A	chr3:49448379-49448669	Hela-S3	cervix:	n/a	n/a
17	CHD1	chr3:49448365-49449347	H1-hESC	embryonic stem cell:	n/a	n/a
18	RELA	chr3:49448514-49450624	GM10847	blood:	n/a	n/a
19	POLR2A	chr3:49448658-49450269	Hela-S3	cervix:	n/a	n/a
20	SIN3AK20	chr3:49448636-49450163	PANC-1	pancreas:	n/a	n/a
21	POLR2A	chr3:49448617-49450854	GM12892	blood:	n/a	n/a
22	TAF1	chr3:49448522-49449068	Hela-S3	cervix:	n/a	n/a
23	TCF12	chr3:49448484-49449103	A549	lung:	n/a	n/a
24	MYC	chr3:49448503-49449987	MCF10A-Er-Src	breast:	n/a	chr3:49448867-49448876 chr3:49448924-49448934 chr3:49449585-49449594
25	GATA1	chr3:49448378-49450207	PBDE	blood:	n/a	n/a
26	SIN3A	chr3:49448407-49450296	H1-hESC	embryonic stem cell:	n/a	n/a
27	MXI1	chr3:49447410-49450981	SK-N-SH	brain:	n/a	n/a
28	MXI1	chr3:49447853-49450922	IMR90	lung:	n/a	n/a
29	HA-E2F1	chr3:49448587-49450150	MCF-7	breast:	n/a	chr3:49448935-49448945 chr3:49449223-49449233 chr3:49449062-49449071

No.	Distal block	Cell Line	Cell type
1	chr3:49447135..49449560-chr3:49709671..49711727,2	K562	blood:
2	chr3:49387350..49389031-chr3:49446931..49448922,3	K562	blood:
3	chr3:49375112..49379681-chr3:49446166..49452291,17	K562	blood:
4	chr3:49203572..49205247-chr3:49448132..49451113,3	MCF-7	breast:
5	chr3:49064721..49066912-chr3:49446904..49449709,2	K562	blood:
6	chr3:49394592..49396828-chr3:49447365..49450223,2	K562	blood:
7	chr3:49130018..49132497-chr3:49447157..49449829,4	K562	blood:
8	chr3:49447402..49451449-chr3:49505916..49509646,7	K562	blood:
9	chr3:49058292..49060438-chr3:49448532..49450849,2	MCF-7	breast:
10	chr3:49375789..49379333-chr3:49446166..49450939,13	K562	blood:
11	chr3:49424540..49427374-chr3:49447605..49449353,2	MCF-7	breast:
12	chr3:49448236..49450769-chr3:49505936..49509558,3	MCF-7	breast:
13	chr3:49377084..49379212-chr3:49447955..49450362,2	MCF-7	breast:
14	chr3:49054710..49056578-chr3:49447542..49450495,2	K562	blood:
15	chr3:49447402..49452044-chr3:49506038..49509646,9	K562	blood:
16	chr3:49129916..49132990-chr3:49447157..49451022,6	K562	blood:
17	chr3:49447469..49451415-chr3:49463621..49468909,12	K562	blood:

Variant related genes	Relation type
TCTA	TF binding region
ENSG00000178057	Chromatin interaction
ENSG00000145029	Chromatin interaction
ENSG00000198218	Chromatin interaction
ENSG00000272434	Chromatin interaction
ENSG00000177352	Chromatin interaction
ENSG00000233276	Chromatin interaction
ENSG00000178035	Chromatin interaction
ENSG00000173402	Chromatin interaction
ENSG00000114316	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000164062	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs11130201	0.89[AFR][1000 genomes]
rs11717485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1522929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1568663	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17080495	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17080510	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17080567	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17080664	0.92[AFR][1000 genomes]
rs1996874	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2131107	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2311794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2311801	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2329024	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28615670	1.00[EUR][1000 genomes]
rs3870334	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3870340	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3912831	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4241409	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4452334	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4527417	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855856	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855857	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855870	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4855872	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855874	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855876	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855879	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55677747	0.81[AFR][1000 genomes]
rs55808753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55990645	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56101322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56760510	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56897974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59579780	0.86[AFR][1000 genomes]
rs60011446	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61749312	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446269	0.97[AFR][1000 genomes]
rs6446270	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446273	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446278	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446279	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446280	0.92[AFR][1000 genomes]
rs6446281	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446282	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446283	1.00[EUR][1000 genomes]
rs6766297	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6787665	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6793124	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6797164	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72936890	1.00[EUR][1000 genomes]
rs73830703	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73830704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73830705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73830706	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831434	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73831435	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73831436	1.00[EUR][1000 genomes]
rs73831437	1.00[EUR][1000 genomes]
rs73831438	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73831439	0.86[AFR][1000 genomes]
rs73831440	0.86[AFR][1000 genomes]
rs73831441	0.86[AFR][1000 genomes]
rs73831442	0.92[AFR][1000 genomes]
rs7646393	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8179172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9311441	1.00[AFR][1000 genomes]
rs9811460	1.00[EUR][1000 genomes]
rs9814413	1.00[EUR][1000 genomes]
rs9830627	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9837396	1.00[EUR][1000 genomes]
rs9849446	1.00[EUR][1000 genomes]
rs9861805	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9869504	1.00[EUR][1000 genomes]
rs9875203	1.00[AMR][1000 genomes];1.00[EUR][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	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49446000-49450200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr3:49446800-49448800	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr3:49446800-49450400	Active TSS	NHLF	lung
4	chr3:49447000-49450200	Active TSS	HSMMtube	muscle
5	chr3:49447000-49450400	Active TSS	Ovary	ovary
6	chr3:49447000-49450600	Active TSS	Aorta	Aorta
7	chr3:49447200-49448800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
8	chr3:49447200-49449400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
9	chr3:49447200-49449800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr3:49447200-49450400	Active TSS	Left Ventricle	heart
11	chr3:49447400-49448800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
12	chr3:49447400-49449800	Active TSS	Fetal Muscle Trunk	muscle
13	chr3:49447400-49450200	Active TSS	Lung	lung
14	chr3:49447400-49450400	Active TSS	H9 Cell Line	embryonic stem cell
15	chr3:49447600-49448800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
16	chr3:49447600-49448800	Weak transcription	Spleen	Spleen
17	chr3:49447600-49449000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
18	chr3:49447600-49450200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr3:49447600-49450400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr3:49447600-49450400	Active TSS	Right Ventricle	heart
21	chr3:49447600-49450400	Active TSS	A549	lung
22	chr3:49447600-49450600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:49447800-49449000	Active TSS	Stomach Mucosa	stomach
24	chr3:49447800-49449200	Active TSS	Right Atrium	heart
25	chr3:49447800-49449800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr3:49447800-49450000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr3:49447800-49450000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
28	chr3:49447800-49450000	Active TSS	Fetal Thymus	thymus
29	chr3:49447800-49450200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr3:49447800-49450200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:49447800-49450200	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr3:49447800-49450200	Active TSS	Rectal Mucosa Donor 31	rectum
33	chr3:49447800-49450400	Active TSS	ES-I3 Cell Line	embryonic stem cell
34	chr3:49447800-49450400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:49447800-49450400	Active TSS	Fetal Kidney	kidney
36	chr3:49447800-49450400	Active TSS	Placenta Amnion	Placenta Amnion
37	chr3:49447800-49450400	Active TSS	GM12878-XiMat	blood
38	chr3:49447800-49450400	Active TSS	NHDF-Ad	bronchial
39	chr3:49448000-49448800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr3:49448000-49449400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:49448000-49449800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr3:49448000-49449800	Active TSS	Colonic Mucosa	Colon
43	chr3:49448000-49450000	Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr3:49448000-49450000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:49448000-49450000	Active TSS	Brain Germinal Matrix	brain
46	chr3:49448000-49450200	Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr3:49448000-49450200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:49448000-49450200	Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr3:49448000-49450200	Active TSS	Muscle Satellite Cultured Cells	--
50	chr3:49448000-49450200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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