Variant report

Variant	rs60611300
Chromosome Location	chr3:52569949-52569950
allele	C/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	MXI1	chr3:52569563-52572387	IMR90	lung:	n/a	n/a
2	MYC	chr3:52569901-52571328	NB4	blood:	n/a	chr3:52571141-52571154 chr3:52571141-52571154 chr3:52571141-52571154
3	REST	chr3:52569917-52571447	H1-neurons	neurons:	n/a	chr3:52570475-52570488 chr3:52570485-52570493 chr3:52570478-52570491
4	MXI1	chr3:52569858-52571439	GM12878	blood:	n/a	n/a
5	SIN3A	chr3:52569895-52571516	H1-hESC	embryonic stem cell:	n/a	chr3:52570478-52570491
6	MXI1	chr3:52569762-52572127	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr3:52569842-52571172	HCT-116	colon:	n/a	n/a
8	ZNF263	chr3:52568872-52571459	HEK293-T-REx	kidney:	n/a	n/a
9	HCFC1	chr3:52569853-52571476	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr3:52560598-52572342	HepG2	liver:	n/a	n/a
11	POLR2A	chr3:52569927-52570942	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52569931..52572827-chr3:52736282..52738188,2	K562	blood:
2	chr3:52488081..52492441-chr3:52568649..52570860,4	K562	blood:
3	chr3:52568115..52572187-chr3:52717267..52721555,8	K562	blood:
4	chr3:52567779..52572340-chr3:52718708..52722750,6	K562	blood:
5	chr16:2014433..2014972-chr3:52569933..52570806,2	NB4	blood:
6	chr3:52554843..52559532-chr3:52566910..52570402,7	MCF-7	breast:
7	chr3:52569842..52571498-chr3:52584728..52587706,2	MCF-7	breast:
8	chr3:52488315..52491899-chr3:52569459..52572680,4	MCF-7	breast:
9	chr3:52539372..52542636-chr3:52569567..52572921,4	MCF-7	breast:
10	chr3:52567553..52570571-chr3:52718365..52721514,3	MCF-7	breast:
11	chr3:52567106..52571736-chr3:52712759..52716604,4	K562	blood:

Variant related genes	Relation type
SMIM4	TF binding region
NT5DC2	TF binding region
ENSG00000114854	Chromatin interaction
ENSG00000252768	Chromatin interaction
ENSG00000163938	Chromatin interaction
ENSG00000010327	Chromatin interaction
ENSG00000163939	Chromatin interaction
ENSG00000140988	Chromatin interaction
ENSG00000255198	Chromatin interaction
ENSG00000168268	Chromatin interaction
ENSG00000010322	Chromatin interaction
ENSG00000016864	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10510759	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12107484	0.89[AFR][1000 genomes]
rs1987234	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs34173244	0.90[AFR][1000 genomes]
rs35920544	0.99[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs56156188	0.84[AFR][1000 genomes]
rs56259931	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs57008939	0.84[AFR][1000 genomes]
rs57246324	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs57298447	0.90[AFR][1000 genomes]
rs57319306	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs57560655	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs57757646	0.89[AFR][1000 genomes]
rs57869735	0.90[AFR][1000 genomes]
rs58100002	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs58725214	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs58924550	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59078569	1.00[ASN][1000 genomes]
rs59410274	1.00[ASN][1000 genomes]
rs60311166	0.87[AFR][1000 genomes]
rs60415551	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs60682984	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60823713	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs60916588	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs61220667	0.83[AFR][1000 genomes]
rs61418167	1.00[ASN][1000 genomes]
rs61538294	0.85[AFR][1000 genomes]
rs6774097	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6780005	0.85[AFR][1000 genomes]
rs6803492	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72947535	0.96[AFR][1000 genomes]
rs72947580	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs72947589	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs72950430	0.85[AFR][1000 genomes]
rs72950432	0.83[AFR][1000 genomes]
rs72965177	0.89[AFR][1000 genomes]
rs72965181	0.92[AFR][1000 genomes]
rs7643568	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7647992	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7648016	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	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
8	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
9	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:126 , 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	chr3:52567600-52570000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr3:52568200-52570600	Weak transcription	Small Intestine	intestine
4	chr3:52568400-52570000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr3:52568400-52570000	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr3:52568400-52570000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr3:52568400-52570000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr3:52568400-52570000	Weak transcription	Thymus	Thymus
9	chr3:52568400-52570400	Flanking Active TSS	K562	blood
10	chr3:52568600-52570000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr3:52568600-52570000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr3:52568600-52570000	Enhancers	Brain Cingulate Gyrus	brain
13	chr3:52568600-52570000	Enhancers	Brain Substantia Nigra	brain
14	chr3:52568600-52570000	Enhancers	Fetal Thymus	thymus
15	chr3:52568600-52570000	Weak transcription	Psoas Muscle	Psoas
16	chr3:52568600-52570200	Enhancers	Placenta	Placenta
17	chr3:52568600-52570600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr3:52568600-52570600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr3:52568600-52570600	Weak transcription	HSMMtube	muscle
20	chr3:52568800-52570000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:52568800-52570000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr3:52568800-52570000	Weak transcription	Liver	Liver
23	chr3:52568800-52570000	Enhancers	Fetal Heart	heart
24	chr3:52568800-52570200	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr3:52568800-52570200	Weak transcription	Aorta	Aorta
26	chr3:52568800-52570600	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr3:52569000-52570000	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr3:52569000-52570000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr3:52569000-52570000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:52569000-52570000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr3:52569000-52570000	Enhancers	Adipose Nuclei	Adipose
32	chr3:52569000-52570000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr3:52569000-52570000	Enhancers	Colon Smooth Muscle	Colon
34	chr3:52569000-52570000	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr3:52569000-52570000	Weak transcription	Rectal Smooth Muscle	rectum
36	chr3:52569000-52570000	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr3:52569000-52570000	Weak transcription	Stomach Mucosa	stomach
38	chr3:52569000-52570000	Weak transcription	A549	lung
39	chr3:52569000-52570000	Enhancers	NHEK	skin
40	chr3:52569000-52570200	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr3:52569000-52570200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:52569000-52570200	Enhancers	Colonic Mucosa	Colon
43	chr3:52569000-52570200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr3:52569000-52570200	Enhancers	Fetal Stomach	stomach
45	chr3:52569000-52570200	Weak transcription	Pancreas	Pancrea
46	chr3:52569000-52570200	Weak transcription	Right Atrium	heart
47	chr3:52569000-52570200	Enhancers	HMEC	breast
48	chr3:52569000-52570200	Weak transcription	HSMM	muscle
49	chr3:52569000-52570600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr3:52569000-52570600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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