Variant report

Variant	rs164636
Chromosome Location	chr3:52265259-52265260
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	POLR2A	chr3:52264353-52265603	K562	blood:	n/a	n/a
2	CTCF	chr3:52265200-52265350	GM12869	blood:	n/a	n/a
3	CTCF	chr3:52264901-52266096	SK-N-SH	brain:	n/a	chr3:52265854-52265863 chr3:52265691-52265704 chr3:52265708-52265717 chr3:52265705-52265718 chr3:52265707-52265728 chr3:52265706-52265722 chr3:52265705-52265723 chr3:52265708-52265721
4	CTCF	chr3:52265160-52265310	NHLF	lung:	n/a	n/a
5	CTCF	chr3:52265240-52265390	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:52263321..52268061-chr3:52310039..52314728,5	K562	blood:
2	chr3:52264729..52268939-chr3:52269297..52274565,7	K562	blood:
3	chr3:52264055..52267306-chr3:52309351..52312799,8	MCF-7	breast:
4	chr3:52262375..52268246-chr3:52270366..52274345,8	K562	blood:
5	chr3:52263787..52265921-chr3:52311180..52314270,4	MCF-7	breast:
6	chr3:52262890..52265555-chr3:52320474..52321976,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173366	TF binding region
ENSG00000168237	Chromatin interaction
ENSG00000164091	Chromatin interaction
ENSG00000243224	Chromatin interaction
ENSG00000239732	Chromatin interaction
ENSG00000247596	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1035002	0.86[AMR][1000 genomes]
rs104902	0.84[ASN][1000 genomes]
rs123598	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs123603	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13060192	0.82[AMR][1000 genomes]
rs13065677	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13071708	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13074649	0.82[AMR][1000 genomes]
rs13076508	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13089892	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13091360	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13093555	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13096571	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13098856	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs164637	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2109557	0.91[AMR][1000 genomes]
rs2215466	0.82[AMR][1000 genomes]
rs2878549	0.82[AMR][1000 genomes]
rs34181173	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34332947	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34385735	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34551211	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34628357	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34827613	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35130772	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs352141	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs352144	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs353545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs353548	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35982798	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3755810	0.91[AMR][1000 genomes]
rs3774409	0.82[AMR][1000 genomes]
rs3796342	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs419050	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs419604	0.91[AMR][1000 genomes]
rs419752	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4687541	0.82[AMR][1000 genomes]
rs498778	0.91[AMR][1000 genomes]
rs575476	0.91[AMR][1000 genomes]
rs61734640	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs676034	0.86[AMR][1000 genomes]
rs6771558	0.82[AMR][1000 genomes]
rs6795333	0.91[AMR][1000 genomes]
rs71297391	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71297394	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71297395	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71297396	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9850471	0.82[AMR][1000 genomes]
rs9855470	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
4	nsv460537	chr3:52148233-52290550	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	nsv590301	chr3:52148233-52290550	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv508218	chr3:52155869-52290410	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
8	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer 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	98 gene(s)	inside rSNPs	diseases
9	nsv876787	chr3:52236762-52367932	Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS 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	90 gene(s)	inside rSNPs	diseases
10	nsv876788	chr3:52247110-52367932	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
11	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
12	nsv876790	chr3:52261382-52286825	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
13	esv3376719	chr3:52263462-52266260	Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52247800-52272200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:52251000-52266600	Weak transcription	Fetal Brain Male	brain
3	chr3:52251600-52266600	Weak transcription	Psoas Muscle	Psoas
4	chr3:52253200-52269600	Weak transcription	Fetal Kidney	kidney
5	chr3:52255000-52268600	Weak transcription	Right Atrium	heart
6	chr3:52255200-52270400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:52259600-52268200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:52260600-52265600	Strong transcription	Esophagus	oesophagus
9	chr3:52261000-52265400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr3:52261000-52265800	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr3:52261000-52266600	Strong transcription	Placenta Amnion	Placenta Amnion
12	chr3:52261000-52269400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr3:52261200-52265600	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr3:52261200-52265800	Strong transcription	Primary T cells from cord blood	blood
15	chr3:52261200-52265800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr3:52261200-52266400	Strong transcription	Lung	lung
17	chr3:52261200-52267000	Strong transcription	Fetal Muscle Trunk	muscle
18	chr3:52261200-52270800	Strong transcription	Fetal Stomach	stomach
19	chr3:52261400-52265600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr3:52261400-52265600	Strong transcription	Liver	Liver
21	chr3:52261400-52269000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:52261400-52269600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:52261600-52265400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr3:52261600-52265400	Strong transcription	Spleen	Spleen
25	chr3:52261600-52265800	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr3:52261600-52266000	Strong transcription	Brain Anterior Caudate	brain
27	chr3:52261600-52266800	Strong transcription	Placenta	Placenta
28	chr3:52261600-52267000	Strong transcription	Gastric	stomach
29	chr3:52261600-52267200	Strong transcription	Fetal Muscle Leg	muscle
30	chr3:52261600-52269800	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr3:52261600-52270000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:52261600-52270000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr3:52261600-52270600	Strong transcription	NHEK	skin
34	chr3:52261800-52265400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr3:52261800-52265400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:52261800-52265400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:52261800-52265400	Strong transcription	Thymus	Thymus
38	chr3:52261800-52265600	Strong transcription	Adipose Nuclei	Adipose
39	chr3:52261800-52265600	Strong transcription	Brain Substantia Nigra	brain
40	chr3:52261800-52265800	Strong transcription	Stomach Smooth Muscle	stomach
41	chr3:52261800-52266000	Strong transcription	Left Ventricle	heart
42	chr3:52261800-52266200	Strong transcription	Brain Cingulate Gyrus	brain
43	chr3:52261800-52266400	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:52261800-52266800	Strong transcription	Fetal Brain Female	brain
45	chr3:52261800-52267200	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr3:52261800-52267800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:52261800-52269400	Strong transcription	Brain Germinal Matrix	brain
48	chr3:52261800-52269800	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr3:52261800-52269800	Strong transcription	Duodenum Mucosa	Duodenum
50	chr3:52261800-52270000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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