Variant report

Variant	rs28370160
Chromosome Location	chr1:223954648-223954649
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:223954584-223954841	U87	brain:	n/a	n/a
2	POLR2A	chr1:223954580-223954790	K562	blood:	n/a	n/a
3	POLR2A	chr1:223954612-223954860	K562	blood:	n/a	n/a
4	POLR2A	chr1:223954557-223954818	K562	blood:	n/a	n/a
5	POLR2A	chr1:223954285-223954807	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr1:223950693-223954959	K562	blood:	n/a	n/a
7	ZNF384	chr1:223954522-223954786	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:223948378..223951598-chr1:223951905..223956257,3	MCF-7	breast:
2	chr1:223946469..223951364-chr1:223952394..223955847,6	K562	blood:
3	chr1:223946962..223949803-chr1:223953280..223955941,2	MCF-7	breast:
4	chr1:223953070..223955896-chr1:224033330..224035597,3	K562	blood:
5	chr1:223944085..223948831-chr1:223951617..223954672,7	K562	blood:
6	chr1:223952715..223955634-chr1:223956735..223959686,2	MCF-7	breast:

No data

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

Extended variants
information (count: 119 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10158199	1.00[EUR][1000 genomes]
rs10158508	1.00[EUR][1000 genomes]
rs10158843	1.00[EUR][1000 genomes]
rs10159010	1.00[EUR][1000 genomes]
rs10159015	0.83[ASN][1000 genomes]
rs1153962	1.00[EUR][1000 genomes]
rs1153966	1.00[EUR][1000 genomes]
rs12022914	0.98[ASN][1000 genomes]
rs12022920	0.98[ASN][1000 genomes]
rs12024059	0.98[ASN][1000 genomes]
rs12025911	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12026548	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12027762	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12028843	0.98[ASN][1000 genomes]
rs12029400	0.81[ASN][1000 genomes]
rs12031089	0.81[ASN][1000 genomes]
rs12031127	0.81[ASN][1000 genomes]
rs12031539	0.81[ASN][1000 genomes]
rs12031859	0.98[ASN][1000 genomes]
rs12032205	0.81[ASN][1000 genomes]
rs12032254	0.81[ASN][1000 genomes]
rs12032570	0.81[ASN][1000 genomes]
rs12033388	0.81[ASN][1000 genomes]
rs12033399	0.81[ASN][1000 genomes]
rs12033405	0.81[ASN][1000 genomes]
rs12034120	0.95[ASN][1000 genomes]
rs12034364	0.81[ASN][1000 genomes]
rs12034534	0.81[ASN][1000 genomes]
rs12034737	0.81[ASN][1000 genomes]
rs12034914	0.95[ASN][1000 genomes]
rs12035506	0.86[ASN][1000 genomes]
rs12036390	0.85[ASN][1000 genomes]
rs12036636	0.81[ASN][1000 genomes]
rs12036693	0.81[ASN][1000 genomes]
rs12036717	0.95[ASN][1000 genomes]
rs12038665	0.98[ASN][1000 genomes]
rs12038706	0.95[ASN][1000 genomes]
rs12039721	0.95[ASN][1000 genomes]
rs12040996	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12043790	0.98[ASN][1000 genomes]
rs12044358	0.98[ASN][1000 genomes]
rs12044652	0.95[ASN][1000 genomes]
rs12044659	0.95[ASN][1000 genomes]
rs12046297	0.81[ASN][1000 genomes]
rs12047342	0.95[ASN][1000 genomes]
rs12047952	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12088254	0.83[ASN][1000 genomes]
rs1222131	1.00[EUR][1000 genomes]
rs12239402	1.00[EUR][1000 genomes]
rs12239445	1.00[EUR][1000 genomes]
rs12239678	1.00[EUR][1000 genomes]
rs13375296	1.00[EUR][1000 genomes]
rs1542507	0.98[ASN][1000 genomes]
rs16842078	1.00[EUR][1000 genomes]
rs16842173	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16842177	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16842201	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16842217	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16842234	1.00[EUR][1000 genomes]
rs16842259	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16842291	1.00[EUR][1000 genomes]
rs16842341	1.00[EUR][1000 genomes]
rs1890119	1.00[EUR][1000 genomes]
rs1981168	0.81[ASN][1000 genomes]
rs1981169	0.81[ASN][1000 genomes]
rs1981170	0.81[ASN][1000 genomes]
rs2230082	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28370064	1.00[EUR][1000 genomes]
rs28370079	1.00[EUR][1000 genomes]
rs28370095	0.95[ASN][1000 genomes]
rs28370099	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28370112	0.95[ASN][1000 genomes]
rs28370115	0.95[ASN][1000 genomes]
rs28370161	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28370162	1.00[EUR][1000 genomes]
rs28370166	0.98[ASN][1000 genomes]
rs28370174	0.98[ASN][1000 genomes]
rs28370177	0.98[ASN][1000 genomes]
rs28370178	0.98[ASN][1000 genomes]
rs28458390	1.00[EUR][1000 genomes]
rs28684725	1.00[EUR][1000 genomes]
rs3754088	0.95[ASN][1000 genomes]
rs3767710	0.98[ASN][1000 genomes]
rs3767712	0.90[ASN][1000 genomes]
rs3767713	0.95[ASN][1000 genomes]
rs3820474	0.98[ASN][1000 genomes]
rs3820481	0.95[ASN][1000 genomes]
rs41345146	1.00[EUR][1000 genomes]
rs56947789	1.00[EUR][1000 genomes]
rs57380389	1.00[EUR][1000 genomes]
rs58753599	1.00[EUR][1000 genomes]
rs59433589	1.00[EUR][1000 genomes]
rs59793743	1.00[EUR][1000 genomes]
rs59948383	1.00[EUR][1000 genomes]
rs59970447	1.00[EUR][1000 genomes]
rs60681980	0.83[ASN][1000 genomes]
rs61437308	0.98[ASN][1000 genomes]
rs61824005	0.83[ASN][1000 genomes]
rs73114413	1.00[EUR][1000 genomes]
rs73125398	1.00[EUR][1000 genomes]
rs73127405	1.00[EUR][1000 genomes]
rs73127411	1.00[EUR][1000 genomes]
rs73127438	1.00[EUR][1000 genomes]
rs73127450	1.00[EUR][1000 genomes]
rs747811	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7515215	1.00[EUR][1000 genomes]
rs7538151	0.95[ASN][1000 genomes]
rs7552702	0.83[ASN][1000 genomes]
rs9286986	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9804140	0.95[ASN][1000 genomes]
rs9970756	1.00[EUR][1000 genomes];0.95[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:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223931200-223954800	Strong transcription	HMEC	breast
2	chr1:223936600-223954800	Strong transcription	NHEK	skin
3	chr1:223937000-223954800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:223937000-223954800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:223937000-223954800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:223937000-223954800	Strong transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:223937000-223954800	Strong transcription	NHDF-Ad	bronchial
8	chr1:223937000-223954800	Strong transcription	Osteobl	bone
9	chr1:223937000-223957200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr1:223937000-223959000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:223937000-223960000	Weak transcription	Thymus	Thymus
12	chr1:223937200-223954800	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr1:223937200-223954800	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr1:223937200-223954800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr1:223937200-223954800	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr1:223937200-223958400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr1:223937200-223958400	Weak transcription	Fetal Heart	heart
18	chr1:223937400-223954800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr1:223937400-223954800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr1:223937400-223954800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:223937400-223954800	Strong transcription	Fetal Stomach	stomach
22	chr1:223937400-223954800	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr1:223937400-223954800	Strong transcription	A549	lung
24	chr1:223937600-223954800	Strong transcription	Stomach Smooth Muscle	stomach
25	chr1:223937800-223954800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr1:223937800-223954800	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr1:223938000-223954800	Strong transcription	Duodenum Mucosa	Duodenum
28	chr1:223938000-223954800	Strong transcription	Fetal Brain Female	brain
29	chr1:223938200-223954800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:223938200-223954800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr1:223938600-223956600	Weak transcription	Fetal Kidney	kidney
32	chr1:223939800-223956600	Weak transcription	Fetal Thymus	thymus
33	chr1:223940800-223954800	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr1:223940800-223955000	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr1:223941000-223954800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr1:223941000-223957600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr1:223941000-223958200	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr1:223941000-223959400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr1:223941200-223961600	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr1:223942400-223958800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr1:223942600-223954800	Strong transcription	Primary T cells from cord blood	blood
42	chr1:223944800-223954800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr1:223947000-223957200	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr1:223948000-223957600	Weak transcription	Fetal Brain Male	brain
45	chr1:223948400-223957200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:223949600-223955000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr1:223949600-223958400	Weak transcription	Small Intestine	intestine
48	chr1:223949800-223954800	Strong transcription	Right Ventricle	heart
49	chr1:223950000-223957600	Weak transcription	Right Atrium	heart
50	chr1:223950200-223957000	Weak transcription	Psoas Muscle	Psoas

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