Variant report

Variant	rs2399481
Chromosome Location	chr3:113234984-113234985
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:42)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:42 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:113233500-113235394	MCF-7	breast:	n/a	n/a
2	RAD21	chr3:113234915-113235410	A549	lung:	n/a	n/a
3	RAD21	chr3:113234970-113235283	HepG2	liver:	n/a	n/a
4	E2F6	chr3:113234418-113235244	A549	lung:	n/a	n/a
5	TCF12	chr3:113233493-113235250	A549	lung:	n/a	chr3:113234598-113234607
6	CTCF	chr3:113234959-113235466	MCF-7	breast:	n/a	n/a
7	RAD21	chr3:113234972-113235309	A549	lung:	n/a	n/a
8	RAD21	chr3:113234807-113235501	MCF-7	breast:	n/a	n/a
9	POLR2A	chr3:113233054-113235426	HepG2	liver:	n/a	n/a
10	CTCF	chr3:113234411-113235485	A549	lung:	n/a	n/a
11	CTCF	chr3:113234954-113235283	HepG2	liver:	n/a	n/a
12	POLR2A	chr3:113233436-113235338	MCF10A-Er-Src	breast:	n/a	n/a
13	RAD21	chr3:113234903-113235258	SK-N-SH_RA	brain:	n/a	n/a
14	CTCF	chr3:113234958-113235319	GM12878	blood:	n/a	n/a
15	RAD21	chr3:113234876-113235331	HepG2	liver:	n/a	n/a
16	RAD21	chr3:113234937-113235306	GM12878	blood:	n/a	n/a
17	MYC	chr3:113234565-113235152	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr3:113233650-113235309	MCF10A-Er-Src	breast:	n/a	n/a
19	SMC3	chr3:113234722-113235483	SK-N-SH	brain:	n/a	n/a
20	CTCF	chr3:113234857-113235369	MCF-7	breast:	n/a	n/a
21	RAD21	chr3:113234867-113235418	MCF-7	breast:	n/a	n/a
22	CTCF	chr3:113234960-113235110	AG10803	skin:	n/a	n/a
23	POLR2A	chr3:113234476-113235365	GM12878	blood:	n/a	n/a
24	CTCF	chr3:113234469-113235507	SK-N-SH	brain:	n/a	n/a
25	MAX	chr3:113234422-113235417	A549	lung:	n/a	n/a
26	RAD21	chr3:113234904-113235421	A549	lung:	n/a	n/a
27	MXI1	chr3:113232708-113235405	SK-N-SH	brain:	n/a	chr3:113234028-113234043
28	POLR2A	chr3:113234972-113235216	HepG2	liver:	n/a	n/a
29	RAD21	chr3:113232623-113235564	SK-N-SH	brain:	n/a	n/a
30	CTCF	chr3:113234964-113235249	T-47D	breast:	n/a	n/a
31	POLR2A	chr3:113234973-113235277	GM12878	blood:	n/a	n/a
32	MAX	chr3:113234491-113235004	SK-N-SH	brain:	n/a	n/a
33	PML	chr3:113234497-113235009	GM12878	blood:	n/a	n/a
34	POLR2A	chr3:113233480-113235120	PBDE	blood:	n/a	n/a
35	MAX	chr3:113234470-113235390	MCF-7	breast:	n/a	n/a
36	POLR2A	chr3:113233411-113235286	GM12891	blood:	n/a	n/a
37	POLR2A	chr3:113233438-113235398	GM12878	blood:	n/a	n/a
38	POLR2A	chr3:113234695-113235096	ProgFib	skin:	n/a	n/a
39	POLR2A	chr3:113233449-113235445	Raji	blood:	n/a	n/a
40	MAX	chr3:113234436-113235049	A549	lung:	n/a	n/a
41	CTCF	chr3:113234953-113235199	A549	lung:	n/a	n/a
42	CTCF	chr3:113234980-113235130	HepG2	liver:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:113229615..113239929-chr3:113247196..113257849,45	MCF-7	breast:
2	chr3:112279637..112281423-chr3:113232414..113235211,2	K562	blood:
3	chr3:113234667..113235687-chr3:113250927..113252564,4	MCF-7	breast:
4	chr3:113232695..113235446-chr3:113249011..113251267,3	K562	blood:
5	chr3:113234276..113236578-chr3:113295557..113299306,4	MCF-7	breast:
6	chr3:113234708..113235305-chr3:113296493..113297174,2	MCF-7	breast:
7	chr3:113234741..113235548-chr3:113270495..113271038,2	MCF-7	breast:
8	chr3:113234941..113235805-chr3:113271441..113271984,2	MCF-7	breast:
9	chr3:113233753..113235613-chr3:113463995..113467002,3	MCF-7	breast:
10	chr3:113232788..113235774-chr3:113464780..113467765,2	MCF-7	breast:

No data

Variant related genes	Relation type
SPICE1	TF binding region
ENSG00000121579	Chromatin interaction
ENSG00000114573	Chromatin interaction
ENSG00000242659	Chromatin interaction
ENSG00000072858	Chromatin interaction
ENSG00000144848	Chromatin interaction
ENSG00000138459	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10934229	0.93[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10934230	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10934233	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10934234	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12054036	0.91[EUR][1000 genomes]
rs12629271	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12629498	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12630518	0.93[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12631929	0.82[EUR][1000 genomes]
rs12632492	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637924	0.85[EUR][1000 genomes]
rs1463644	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16860899	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs2271495	0.82[EUR][1000 genomes]
rs2291413	0.86[CEU][hapmap];0.83[CHB][hapmap]
rs2306069	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732804	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3896909	0.81[EUR][1000 genomes]
rs4682137	0.93[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4682485	0.93[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap]
rs4682489	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55757335	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55865352	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60292736	0.86[AFR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62265992	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62265996	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6809516	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs73237104	0.85[EUR][1000 genomes]
rs73237110	0.85[EUR][1000 genomes]
rs73237123	0.85[EUR][1000 genomes]
rs73237130	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73237143	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73239107	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73239126	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7637206	0.82[EUR][1000 genomes]
rs7643592	0.87[CHB][hapmap]
rs7643843	0.87[CHB][hapmap]
rs7647220	0.83[CHB][hapmap]
rs7653186	0.83[CHB][hapmap]
rs8179926	0.85[EUR][1000 genomes]
rs9820386	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9857414	0.91[CHB][hapmap];0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv1004000	chr3:113116778-113513899	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv877349	chr3:113208224-113323787	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
4	nsv877350	chr3:113208224-113332235	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113232400-113235200	Active TSS	A549	lung
2	chr3:113232600-113235000	Active TSS	Thymus	Thymus
3	chr3:113232600-113235000	Active TSS	NHLF	lung
4	chr3:113232800-113235000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:113232800-113235200	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr3:113233000-113235000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:113233000-113235000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:113233000-113235000	Active TSS	Right Atrium	heart
9	chr3:113233000-113235200	Active TSS	Rectal Mucosa Donor 29	rectum
10	chr3:113233000-113235400	Active TSS	Psoas Muscle	Psoas
11	chr3:113233200-113235000	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr3:113233200-113235000	Active TSS	Colonic Mucosa	Colon
13	chr3:113233200-113235200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:113233400-113235000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:113233400-113235000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:113233400-113235000	Active TSS	Primary T killer memory cells from peripheral blood	blood
17	chr3:113233400-113235000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:113233400-113235000	Active TSS	Brain Inferior Temporal Lobe	brain
19	chr3:113233400-113235000	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr3:113233400-113235200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:113233400-113235200	Active TSS	Brain Anterior Caudate	brain
22	chr3:113233400-113235200	Active TSS	Fetal Lung	lung
23	chr3:113233400-113235400	Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr3:113233600-113235000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
25	chr3:113233600-113235000	Active TSS	HUVEC	blood vessel
26	chr3:113233600-113235200	Active TSS	Brain Angular Gyrus	brain
27	chr3:113233800-113235000	Active TSS	Rectal Mucosa Donor 31	rectum
28	chr3:113234400-113235000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr3:113234400-113235000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr3:113234400-113235000	Enhancers	Spleen	Spleen
31	chr3:113234400-113235200	Flanking Active TSS	Primary B cells from cord blood	blood
32	chr3:113234400-113235600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:113234600-113235000	Flanking Active TSS	Primary B cells from peripheral blood	blood
34	chr3:113234600-113235000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
35	chr3:113234600-113235000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr3:113234600-113235000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr3:113234600-113235000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
38	chr3:113234600-113235000	Flanking Active TSS	Brain Substantia Nigra	brain
39	chr3:113234600-113235000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr3:113234600-113235000	Flanking Active TSS	Placenta	Placenta
41	chr3:113234600-113235000	Flanking Active TSS	Hela-S3	cervix
42	chr3:113234600-113235000	Flanking Active TSS	HepG2	liver
43	chr3:113234600-113235200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:113234600-113235200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
45	chr3:113234600-113235200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr3:113234600-113235200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:113234600-113235200	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr3:113234600-113235200	Flanking Active TSS	GM12878-XiMat	blood
49	chr3:113234600-113235200	Flanking Active TSS	Osteobl	bone
50	chr3:113234600-113235400	Flanking Active TSS	Primary T cells from cord blood	blood

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