Variant report

Variant	rs6446279
Chromosome Location	chr3:49509292-49509293
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr3:49506252-49509681	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr3:49509279-49509684	K562	blood:	n/a	n/a
3	HCFC1	chr3:49506744-49509311	Hela-S3	cervix:	n/a	n/a
4	MAX	chr3:49509177-49509695	K562	blood:	n/a	chr3:49509620-49509630
5	ZNF263	chr3:49509236-49509916	HEK293-T-REx	kidney:	n/a	chr3:49509743-49509752
6	MYC	chr3:49509287-49509814	K562	blood:	n/a	chr3:49509620-49509630
7	POLR2A	chr3:49509196-49509804	PBDE	blood:	n/a	n/a
8	POLR2A	chr3:49509198-49509889	K562	blood:	n/a	n/a
9	MAZ	chr3:49506361-49509347	IMR90	lung:	n/a	chr3:49507013-49507023 chr3:49509096-49509107
10	NR2F2	chr3:49509168-49509966	K562	blood:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49506494..49510419-chr3:49709515..49713189,4	MCF-7	breast:
2	chr3:49507792..49509395-chr3:49538517..49540372,2	MCF-7	breast:
3	chr3:49506988..49509379-chr3:49529279..49532110,2	MCF-7	breast:
4	chr3:49447402..49451449-chr3:49505916..49509646,7	K562	blood:
5	chr3:49506444..49509653-chr3:49710909..49714606,3	K562	blood:
6	chr3:49056423..49060378-chr3:49506507..49510634,4	K562	blood:
7	chr3:49447402..49452044-chr3:49506038..49509646,9	K562	blood:
8	chr3:49130007..49132020-chr3:49507888..49509693,2	K562	blood:
9	chr3:49448236..49450769-chr3:49505936..49509558,3	MCF-7	breast:
10	chr3:49448736..49451146-chr3:49507489..49509395,2	MCF-7	breast:
11	chr3:49507807..49509484-chr3:49555798..49559257,3	MCF-7	breast:
12	chr3:49507938..49509712-chr3:49512685..49515016,2	K562	blood:
13	chr3:49376524..49378988-chr3:49507303..49509521,2	MCF-7	breast:
14	chr3:49508269..49511222-chr3:49551619..49554342,2	K562	blood:
15	chr3:49455358..49458192-chr3:49507443..49509538,2	MCF-7	breast:

No data

Variant related genes	Relation type
RNA5SP130	TF binding region
ENSG00000114316	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000067560	Chromatin interaction
ENSG00000164062	Chromatin interaction
ENSG00000198218	Chromatin interaction
ENSG00000173402	Chromatin interaction
ENSG00000207605	Chromatin interaction
ENSG00000145020	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000199032	Chromatin interaction
ENSG00000145022	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs11130201	0.94[AFR][1000 genomes]
rs11717485	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1522929	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1568663	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17080495	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17080510	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17080567	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17080664	0.97[AFR][1000 genomes]
rs1996874	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2131107	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2311794	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2311801	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2329024	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3870334	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3870340	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3912831	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4241409	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4452334	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855856	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855857	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855870	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4855872	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855874	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855875	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855876	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855878	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855879	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55808753	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55990645	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56101322	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56760510	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56897974	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59579780	0.92[AFR][1000 genomes]
rs60011446	0.94[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	0.92[AFR][1000 genomes]
rs6446270	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446271	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446273	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446276	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446278	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446280	0.97[AFR][1000 genomes]
rs6446281	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446282	0.92[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	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6793124	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6797164	1.00[AMR][1000 genomes]
rs73830703	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73830704	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73830705	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73830706	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831434	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73831435	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73831436	1.00[EUR][1000 genomes]
rs73831437	1.00[EUR][1000 genomes]
rs73831438	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73831439	0.92[AFR][1000 genomes]
rs73831440	0.92[AFR][1000 genomes]
rs73831441	0.92[AFR][1000 genomes]
rs73831442	0.97[AFR][1000 genomes]
rs73834006	0.84[AFR][1000 genomes]
rs7646393	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8179172	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9311441	0.94[AFR][1000 genomes]
rs9830627	1.00[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]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	esv3420339	chr3:49505548-49510046	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49506400-49509600	Active TSS	H9 Cell Line	embryonic stem cell
2	chr3:49507400-49509400	Active TSS	HSMM	muscle
3	chr3:49507400-49509400	Active TSS	HSMMtube	muscle
4	chr3:49508200-49509400	Flanking Active TSS	Dnd41	blood
5	chr3:49508200-49509600	Flanking Active TSS	Brain Anterior Caudate	brain
6	chr3:49508200-49510000	Flanking Active TSS	Stomach Smooth Muscle	stomach
7	chr3:49508400-49509400	Flanking Active TSS	Liver	Liver
8	chr3:49508400-49509400	Weak transcription	Spleen	Spleen
9	chr3:49508400-49509400	Flanking Active TSS	NHEK	skin
10	chr3:49508400-49509600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:49508400-49509600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:49508400-49509600	Flanking Active TSS	Brain Angular Gyrus	brain
13	chr3:49508400-49509600	Flanking Active TSS	Brain Cingulate Gyrus	brain
14	chr3:49508400-49510000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
15	chr3:49508600-49509400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
16	chr3:49508600-49509400	Flanking Active TSS	Colon Smooth Muscle	Colon
17	chr3:49508600-49509400	Flanking Active TSS	Fetal Intestine Large	intestine
18	chr3:49508600-49509600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:49508600-49509600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:49508600-49509600	Flanking Active TSS	Fetal Brain Female	brain
21	chr3:49508600-49509600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
22	chr3:49508600-49509800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:49508600-49509800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr3:49508600-49509800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr3:49508600-49509800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr3:49508600-49509800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:49508600-49509800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr3:49508600-49509800	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr3:49508600-49509800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
30	chr3:49508600-49509800	Flanking Active TSS	Fetal Heart	heart
31	chr3:49508600-49509800	Flanking Active TSS	GM12878-XiMat	blood
32	chr3:49508600-49509800	Flanking Active TSS	Osteobl	bone
33	chr3:49508600-49510000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr3:49508600-49510000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr3:49508600-49510000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
36	chr3:49508600-49510000	Flanking Active TSS	Rectal Smooth Muscle	rectum
37	chr3:49508600-49510000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr3:49508600-49510000	Flanking Active TSS	Hela-S3	cervix
39	chr3:49508800-49509400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr3:49508800-49509400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
41	chr3:49508800-49509400	Enhancers	Primary neutrophils fromperipheralblood	blood
42	chr3:49508800-49509400	Enhancers	Primary B cells from peripheral blood	blood
43	chr3:49508800-49509400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr3:49508800-49509600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr3:49508800-49509600	Enhancers	Placenta Amnion	Placenta Amnion
46	chr3:49508800-49509600	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr3:49508800-49509800	Enhancers	Primary hematopoietic stem cells	blood
48	chr3:49508800-49509800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
49	chr3:49508800-49509800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
50	chr3:49508800-49509800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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