Variant report

Variant	rs28370159
Chromosome Location	chr1:223954617-223954618
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 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	BCL3	chr1:223952911-223954621	K562	blood:	n/a	n/a
4	POLR2A	chr1:223954612-223954860	K562	blood:	n/a	n/a
5	POLR2A	chr1:223954557-223954818	K562	blood:	n/a	n/a
6	POLR2A	chr1:223954285-223954807	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr1:223950693-223954959	K562	blood:	n/a	n/a
8	ZNF384	chr1:223954522-223954786	K562	blood:	n/a	n/a

No data

(count:7 , 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:
7	chr1:223953008..223954619-chr1:223955987..223958231,2	K562	blood:

No data

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

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10159015	0.81[EUR][1000 genomes]
rs10465524	0.81[EUR][1000 genomes]
rs10503144	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10915707	0.82[EUR][1000 genomes]
rs10915715	0.85[EUR][1000 genomes]
rs1153958	0.81[EUR][1000 genomes]
rs1153965	0.92[EUR][1000 genomes]
rs12046297	0.82[EUR][1000 genomes]
rs12059128	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12059770	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12060361	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12069561	0.82[EUR][1000 genomes]
rs12080250	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12088254	0.91[EUR][1000 genomes]
rs12091841	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1222134	0.82[EUR][1000 genomes]
rs1222138	0.81[EUR][1000 genomes]
rs12562109	0.82[EUR][1000 genomes]
rs12563291	0.87[EUR][1000 genomes]
rs12563477	0.96[EUR][1000 genomes]
rs12563637	0.84[EUR][1000 genomes]
rs12563713	0.89[EUR][1000 genomes]
rs12564557	1.00[ASN][1000 genomes]
rs12565202	1.00[ASN][1000 genomes]
rs12565573	1.00[ASN][1000 genomes]
rs12565967	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12566817	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16841190	1.00[ASN][1000 genomes]
rs16842162	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16842229	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16842257	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16842326	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16842343	1.00[ASN][1000 genomes]
rs17597	0.87[EUR][1000 genomes]
rs17598	0.82[EUR][1000 genomes]
rs17600	0.82[EUR][1000 genomes]
rs28370069	0.89[EUR][1000 genomes]
rs28370073	0.93[EUR][1000 genomes]
rs28370074	0.93[EUR][1000 genomes]
rs28370088	0.93[EUR][1000 genomes]
rs28370170	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34683843	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36032024	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738373	0.82[EUR][1000 genomes]
rs3738374	0.82[EUR][1000 genomes]
rs3738375	0.82[EUR][1000 genomes]
rs3767716	0.83[EUR][1000 genomes]
rs3767717	0.82[EUR][1000 genomes]
rs3767718	0.82[EUR][1000 genomes]
rs3885657	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41303996	1.00[ASN][1000 genomes]
rs58774026	1.00[ASN][1000 genomes]
rs61823580	0.90[EUR][1000 genomes]
rs61823581	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823583	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823585	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823587	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823591	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61824003	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61824005	0.91[EUR][1000 genomes]
rs61824008	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604724	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604727	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604728	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604729	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604730	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658954	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6665485	0.83[EUR][1000 genomes]
rs6674846	0.82[EUR][1000 genomes]
rs6678365	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6682964	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6685557	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691315	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6694960	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696053	0.81[EUR][1000 genomes]
rs6696222	1.00[ASN][1000 genomes]
rs6700366	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73116425	1.00[ASN][1000 genomes]
rs73116447	1.00[ASN][1000 genomes]
rs73116451	1.00[ASN][1000 genomes]
rs73116456	1.00[ASN][1000 genomes]
rs7331	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7515821	1.00[ASN][1000 genomes]
rs7528455	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7530328	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533551	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535882	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552702	0.81[EUR][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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