Variant report

Variant	rs6774097
Chromosome Location	chr3:52569480-52569481
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF263	chr3:52568872-52571459	HEK293-T-REx	kidney:	n/a	n/a
2	POLR2A	chr3:52560598-52572342	HepG2	liver:	n/a	n/a
3	MXI1	chr3:52566005-52569515	SK-N-SH	brain:	n/a	chr3:52566058-52566067

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52488081..52492441-chr3:52568649..52570860,4	K562	blood:
2	chr3:52568115..52572187-chr3:52717267..52721555,8	K562	blood:
3	chr3:52567779..52572340-chr3:52718708..52722750,6	K562	blood:
4	chr3:52554843..52559532-chr3:52566910..52570402,7	MCF-7	breast:
5	chr3:52488315..52491899-chr3:52569459..52572680,4	MCF-7	breast:
6	chr3:52567315..52569798-chr3:52739141..52741499,3	MCF-7	breast:
7	chr3:52567553..52570571-chr3:52718365..52721514,3	MCF-7	breast:
8	chr3:52567106..52571736-chr3:52712759..52716604,4	K562	blood:
9	chr3:52566406..52569677-chr3:52718507..52721358,5	MCF-7	breast:

No data

Variant related genes	Relation type
NT5DC2	TF binding region
SMIM4	TF binding region
ENSG00000016864	Chromatin interaction
ENSG00000163938	Chromatin interaction
ENSG00000168268	Chromatin interaction
ENSG00000010322	Chromatin interaction
ENSG00000010327	Chromatin interaction
ENSG00000114902	Chromatin interaction
ENSG00000114854	Chromatin interaction
ENSG00000163939	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10510759	1.00[TSI][hapmap]
rs12107484	1.00[TSI][hapmap]
rs17052357	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs2028220	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4532127	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs58924550	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59078569	1.00[ASN][1000 genomes]
rs59410274	1.00[ASN][1000 genomes]
rs60611300	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60682984	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61418167	1.00[ASN][1000 genomes]
rs6803492	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72947583	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72947584	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7643568	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7645785	0.80[AMR][1000 genomes]
rs934839	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	esv1818902	chr3:52481406-52572056	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
7	nsv590305	chr3:52535586-52569480	Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv590307	chr3:52540773-52572056	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv876795	chr3:52544470-52572056	Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
10	nsv876796	chr3:52549676-52572056	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 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	chr3:52566200-52571600	Active TSS	Fetal Kidney	kidney
2	chr3:52567200-52569800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr3:52567600-52570000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr3:52568200-52569800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr3:52568200-52569800	Weak transcription	Hela-S3	cervix
6	chr3:52568200-52570600	Weak transcription	Small Intestine	intestine
7	chr3:52568400-52569800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr3:52568400-52569800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr3:52568400-52570000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr3:52568400-52570000	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr3:52568400-52570000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr3:52568400-52570000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr3:52568400-52570000	Weak transcription	Thymus	Thymus
14	chr3:52568400-52570400	Flanking Active TSS	K562	blood
15	chr3:52568600-52569600	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr3:52568600-52569800	Weak transcription	Primary T cells from cord blood	blood
17	chr3:52568600-52569800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr3:52568600-52570000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr3:52568600-52570000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr3:52568600-52570000	Enhancers	Brain Cingulate Gyrus	brain
21	chr3:52568600-52570000	Enhancers	Brain Substantia Nigra	brain
22	chr3:52568600-52570000	Enhancers	Fetal Thymus	thymus
23	chr3:52568600-52570000	Weak transcription	Psoas Muscle	Psoas
24	chr3:52568600-52570200	Enhancers	Placenta	Placenta
25	chr3:52568600-52570600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr3:52568600-52570600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr3:52568600-52570600	Weak transcription	HSMMtube	muscle
28	chr3:52568800-52569800	Weak transcription	Primary B cells from cord blood	blood
29	chr3:52568800-52569800	Weak transcription	Primary B cells from peripheral blood	blood
30	chr3:52568800-52569800	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr3:52568800-52569800	Enhancers	Brain Anterior Caudate	brain
32	chr3:52568800-52569800	Weak transcription	Duodenum Mucosa	Duodenum
33	chr3:52568800-52569800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr3:52568800-52569800	Weak transcription	GM12878-XiMat	blood
35	chr3:52568800-52569800	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr3:52568800-52570000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:52568800-52570000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr3:52568800-52570000	Weak transcription	Liver	Liver
39	chr3:52568800-52570000	Enhancers	Fetal Heart	heart
40	chr3:52568800-52570200	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr3:52568800-52570200	Weak transcription	Aorta	Aorta
42	chr3:52568800-52570600	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr3:52569000-52569600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr3:52569000-52569600	Enhancers	Ovary	ovary
45	chr3:52569000-52569800	Weak transcription	Brain Hippocampus Middle	brain
46	chr3:52569000-52569800	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr3:52569000-52570000	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr3:52569000-52570000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr3:52569000-52570000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr3:52569000-52570000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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