Variant report

Variant	rs28370166
Chromosome Location	chr1:223957669-223957670
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:223957114-223958466	U87	brain:	n/a	n/a
2	POLR2A	chr1:223956590-223957719	K562	blood:	n/a	n/a
3	POLR2A	chr1:223956518-223969626	K562	blood:	n/a	n/a
4	POLR2A	chr1:223957476-223957734	U87	brain:	n/a	n/a
5	POLR2A	chr1:223957232-223957871	K562	blood:	n/a	n/a
6	POLR2A	chr1:223957277-223958402	U87	brain:	n/a	n/a
7	POLR2A	chr1:223957478-223957734	U87	brain:	n/a	n/a
8	POLR2A	chr1:223957660-223957712	HepG2	liver:	n/a	n/a
9	POLR2A	chr1:223956762-223960838	A549	lung:	n/a	n/a
10	POLR2A	chr1:223957635-223958116	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr1:223957290-223957691	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr1:223957191-223958448	HUVEC	blood vessel:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:223898558..223902080-chr1:223957242..223958839,3	K562	blood:
2	chr1:223957411..223959662-chr1:224032167..224034658,2	MCF-7	breast:
3	chr1:223898558..223902031-chr1:223957339..223960421,3	K562	blood:
4	chr1:223888744..223890349-chr1:223956680..223958231,2	MCF-7	breast:

No data

Variant related genes	Relation type
CAPN2	TF binding region
ENSG00000143514	Chromatin interaction
ENSG00000162909	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10159015	0.81[ASN][1000 genomes]
rs12022914	0.95[ASN][1000 genomes]
rs12022920	0.95[ASN][1000 genomes]
rs12024059	0.95[ASN][1000 genomes]
rs12025911	0.81[ASN][1000 genomes]
rs12026548	1.00[ASN][1000 genomes]
rs12027762	0.81[ASN][1000 genomes]
rs12028843	0.95[ASN][1000 genomes]
rs12031859	0.95[ASN][1000 genomes]
rs12034120	0.93[ASN][1000 genomes]
rs12034914	0.93[ASN][1000 genomes]
rs12035506	0.83[ASN][1000 genomes]
rs12036390	0.83[ASN][1000 genomes]
rs12036717	0.93[ASN][1000 genomes]
rs12038665	0.95[ASN][1000 genomes]
rs12038706	0.93[ASN][1000 genomes]
rs12039721	0.93[ASN][1000 genomes]
rs12040996	0.93[ASN][1000 genomes]
rs12043790	1.00[ASN][1000 genomes]
rs12044358	1.00[ASN][1000 genomes]
rs12044652	0.93[ASN][1000 genomes]
rs12044659	0.93[ASN][1000 genomes]
rs12047342	0.93[ASN][1000 genomes]
rs12047952	0.81[ASN][1000 genomes]
rs12088254	0.85[ASN][1000 genomes]
rs1542507	0.95[ASN][1000 genomes]
rs16842259	0.95[ASN][1000 genomes]
rs28370095	0.93[ASN][1000 genomes]
rs28370112	0.93[ASN][1000 genomes]
rs28370115	0.93[ASN][1000 genomes]
rs28370160	0.98[ASN][1000 genomes]
rs28370174	1.00[ASN][1000 genomes]
rs28370177	1.00[ASN][1000 genomes]
rs28370178	1.00[ASN][1000 genomes]
rs3754088	0.93[ASN][1000 genomes]
rs3767710	1.00[ASN][1000 genomes]
rs3767712	0.93[ASN][1000 genomes]
rs3767713	0.93[ASN][1000 genomes]
rs3820474	0.95[ASN][1000 genomes]
rs3820481	0.93[ASN][1000 genomes]
rs60681980	0.81[ASN][1000 genomes]
rs61437308	0.95[ASN][1000 genomes]
rs61824005	0.85[ASN][1000 genomes]
rs747811	1.00[ASN][1000 genomes]
rs7538151	0.93[ASN][1000 genomes]
rs7552702	0.81[ASN][1000 genomes]
rs9804140	0.93[ASN][1000 genomes]
rs9970756	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking 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 target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 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	chr1:223937000-223959000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:223937000-223960000	Weak transcription	Thymus	Thymus
3	chr1:223937200-223958400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr1:223937200-223958400	Weak transcription	Fetal Heart	heart
5	chr1:223941000-223958200	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr1:223941000-223959400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr1:223941200-223961600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:223942400-223958800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:223949600-223958400	Weak transcription	Small Intestine	intestine
10	chr1:223954200-223958800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr1:223954400-223958600	Weak transcription	Ovary	ovary
12	chr1:223954400-223961800	Weak transcription	HepG2	liver
13	chr1:223954800-223964000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:223956400-223958400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:223956600-223957800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:223956600-223957800	ZNF genes & repeats	Fetal Thymus	thymus
17	chr1:223956600-223957800	Strong transcription	A549	lung
18	chr1:223956600-223958000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:223956600-223958000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:223956600-223958000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:223956600-223958000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr1:223956600-223958000	Strong transcription	NH-A	brain
23	chr1:223956600-223958200	Strong transcription	Fetal Intestine Small	intestine
24	chr1:223956600-223958200	Strong transcription	Stomach Mucosa	stomach
25	chr1:223956600-223958400	Strong transcription	Gastric	stomach
26	chr1:223956600-223958400	Strong transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:223956600-223958600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:223956600-223958600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:223956600-223958600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:223956600-223958600	Strong transcription	Colon Smooth Muscle	Colon
31	chr1:223956600-223958600	Strong transcription	Duodenum Mucosa	Duodenum
32	chr1:223956600-223958600	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr1:223956600-223958600	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr1:223956600-223958600	Strong transcription	Stomach Smooth Muscle	stomach
35	chr1:223956600-223958600	Strong transcription	HMEC	breast
36	chr1:223956600-223958800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:223956600-223958800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:223956600-223958800	Weak transcription	Primary B cells from cord blood	blood
39	chr1:223956600-223958800	Strong transcription	Fetal Muscle Trunk	muscle
40	chr1:223956600-223958800	Strong transcription	Fetal Muscle Leg	muscle
41	chr1:223956600-223959000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr1:223956600-223959000	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:223956600-223959000	Strong transcription	Brain Anterior Caudate	brain
44	chr1:223956600-223959000	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr1:223956600-223959200	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr1:223956600-223959200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr1:223956600-223959200	Strong transcription	Fetal Kidney	kidney
48	chr1:223956600-223959200	Strong transcription	Fetal Lung	lung
49	chr1:223956600-223959400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr1:223956600-223959400	Strong transcription	Rectal Smooth Muscle	rectum

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