Variant report

Variant	rs28370061
Chromosome Location	chr1:223936201-223936202
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	E2F6	chr1:223936187-223937113	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:223936046-223936267	HCT-116	colon:	n/a	n/a
3	FOS	chr1:223936030-223936211	MCF10A-Er-Src	breast:	n/a	n/a
4	FOSL2	chr1:223935698-223936405	A549	lung:	n/a	n/a
5	POLR2A	chr1:223934367-223937187	U87	brain:	n/a	n/a
6	POLR2A	chr1:223936100-223936589	GM12892	blood:	n/a	n/a
7	TCF12	chr1:223935446-223937415	A549	lung:	n/a	chr1:223935761-223935771
8	RCOR1	chr1:223934896-223937499	IMR90	lung:	n/a	n/a
9	FOSL2	chr1:223935749-223936315	A549	lung:	n/a	n/a
10	MAX	chr1:223935695-223937237	A549	lung:	n/a	chr1:223935767-223935777 chr1:223935751-223935761
11	POLR2A	chr1:223935571-223936236	K562	blood:	n/a	n/a
12	MAZ	chr1:223934794-223937231	IMR90	lung:	n/a	chr1:223935767-223935777 chr1:223935751-223935761
13	CTCF	chr1:223936188-223936307	IMR90	lung:	n/a	n/a
14	EP300	chr1:223935658-223936411	A549	lung:	n/a	chr1:223935752-223935768
15	POLR2A	chr1:223935939-223936650	IMR90	lung:	n/a	n/a
16	FOS	chr1:223935871-223936401	HUVEC	blood vessel:	n/a	n/a
17	SP1	chr1:223935624-223936457	A549	lung:	n/a	n/a
18	POLR2A	chr1:223934506-223937545	K562	blood:	n/a	n/a
19	MAX	chr1:223936111-223937071	H1-hESC	embryonic stem cell:	n/a	n/a
20	FOS	chr1:223935795-223936264	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr1:223936118-223936246	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr1:223936132-223936415	HUVEC	blood vessel:	n/a	n/a
23	POLR2A	chr1:223935791-223936423	PANC-1	pancreas:	n/a	n/a
24	MAFK	chr1:223936091-223936325	IMR90	lung:	n/a	n/a
25	POLR2A	chr1:223935639-223937214	HUVEC	blood vessel:	n/a	n/a
26	POLR2A	chr1:223935361-223936798	K562	blood:	n/a	n/a
27	FOXA2	chr1:223935874-223936590	A549	lung:	n/a	n/a
28	MAX	chr1:223936197-223937109	H1-hESC	embryonic stem cell:	n/a	n/a
29	CHD2	chr1:223936109-223937115	H1-hESC	embryonic stem cell:	n/a	n/a
30	TBL1XR1	chr1:223936133-223936326	GM12878	blood:	n/a	n/a
31	FOXA2	chr1:223935922-223936498	A549	lung:	n/a	n/a
32	MXI1	chr1:223935038-223937318	IMR90	lung:	n/a	n/a
33	JUND	chr1:223936107-223936217	K562	blood:	n/a	n/a
34	E2F6	chr1:223936127-223937242	H1-hESC	embryonic stem cell:	n/a	n/a
35	GATA2	chr1:223935827-223936278	HUVEC	blood vessel:	n/a	chr1:223936006-223936016 chr1:223936202-223936211 chr1:223935997-223936014 chr1:223936003-223936019 chr1:223936008-223936015 chr1:223936008-223936015 chr1:223936147-223936160 chr1:223936008-223936015
36	E2F6	chr1:223936138-223937261	A549	lung:	n/a	n/a
37	FOS	chr1:223936161-223936235	MCF10A-Er-Src	breast:	n/a	n/a
38	MAX	chr1:223935584-223937348	A549	lung:	n/a	chr1:223935767-223935777 chr1:223935751-223935761
39	FOXP2	chr1:223936108-223936398	PFSK-1	brain:	n/a	n/a
40	NFIC	chr1:223935567-223936256	SK-N-SH	brain:	n/a	n/a
41	POLR2A	chr1:223934529-223937422	A549	lung:	n/a	n/a
42	NR3C1	chr1:223935706-223936394	A549	lung:	n/a	chr1:223936201-223936210
43	POLR2A	chr1:223934361-223937268	U87	brain:	n/a	n/a
44	POLR2A	chr1:223936194-223936426	A549	lung:	n/a	n/a
45	BATF	chr1:223936084-223936283	GM12878	blood:	n/a	chr1:223936201-223936212 chr1:223936202-223936212
46	RAD21	chr1:223936017-223937318	IMR90	lung:	n/a	n/a
47	CEBPB	chr1:223935623-223936433	A549	lung:	n/a	n/a
48	BATF	chr1:223936096-223936303	GM12878	blood:	n/a	chr1:223936201-223936212 chr1:223936202-223936212

No.	Distal block	Cell Line	Cell type
1	chr1:223935650..223937154-chr1:223966505..223968008,2	MCF-7	breast:
2	chr1:223884441..223887114-chr1:223935723..223937532,2	MCF-7	breast:
3	chr1:223887852..223890245-chr1:223935483..223937346,2	MCF-7	breast:
4	chr1:223897059..223902247-chr1:223935403..223939761,6	K562	blood:
5	chr1:223886106..223889532-chr1:223933715..223936535,3	K562	blood:
6	chr1:223898965..223904523-chr1:223935616..223939096,7	MCF-7	breast:
7	chr1:223884772..223887549-chr1:223936018..223938654,2	MCF-7	breast:
8	chr1:223899274..223906539-chr1:223934896..223938666,15	MCF-7	breast:

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

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs28370034	1.00[AMR][1000 genomes]
rs28370036	1.00[AMR][1000 genomes]
rs28370040	1.00[AMR][1000 genomes]
rs28370049	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370059	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73114418	1.00[AMR][1000 genomes]
rs73123604	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73123608	1.00[AMR][1000 genomes]
rs73123609	1.00[AMR][1000 genomes]
rs73125992	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73127441	1.00[AMR][1000 genomes]
rs73128034	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv520609	chr1:223931411-223947081	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
8	nsv521758	chr1:223931411-223954080	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS 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	2 gene(s)	inside rSNPs	n/a
9	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
10	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	chr1:223921600-223936600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:223928000-223936400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr1:223931200-223954800	Strong transcription	HMEC	breast
4	chr1:223931400-223954400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:223932200-223936400	Genic enhancers	NHLF	lung
6	chr1:223932600-223936400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:223933000-223937000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:223933400-223936400	Weak transcription	Thymus	Thymus
9	chr1:223934400-223936400	Genic enhancers	Lung	lung
10	chr1:223934600-223936600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:223934600-223937000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:223934600-223937000	Genic enhancers	NHDF-Ad	bronchial
13	chr1:223934800-223936400	Genic enhancers	Fetal Muscle Leg	muscle
14	chr1:223934800-223936400	Genic enhancers	Fetal Stomach	stomach
15	chr1:223934800-223936600	Genic enhancers	NHEK	skin
16	chr1:223934800-223937000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:223934800-223937000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:223934800-223937400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:223935000-223936400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr1:223935000-223937000	Genic enhancers	Placenta Amnion	Placenta Amnion
21	chr1:223935200-223936400	Weak transcription	Primary T cells from cord blood	blood
22	chr1:223935200-223936400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:223935200-223936400	Weak transcription	Psoas Muscle	Psoas
24	chr1:223935200-223936400	Enhancers	HUVEC	blood vessel
25	chr1:223935200-223936600	Enhancers	Pancreas	Pancrea
26	chr1:223935200-223936800	Genic enhancers	HSMM	muscle
27	chr1:223935200-223937000	Weak transcription	Hela-S3	cervix
28	chr1:223935200-223937200	Enhancers	Fetal Heart	heart
29	chr1:223935400-223936400	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr1:223935400-223936400	Genic enhancers	Fetal Intestine Small	intestine
31	chr1:223935400-223936400	Weak transcription	Fetal Kidney	kidney
32	chr1:223935400-223936400	Genic enhancers	Gastric	stomach
33	chr1:223935400-223936600	Genic enhancers	Sigmoid Colon	Sigmoid Colon
34	chr1:223935400-223936800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr1:223935400-223937000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr1:223935400-223937000	Genic enhancers	Osteobl	bone
37	chr1:223935400-223937400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr1:223935400-223937400	Genic enhancers	Muscle Satellite Cultured Cells	--
39	chr1:223935600-223936400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:223935600-223936400	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr1:223935600-223936400	Enhancers	Brain Angular Gyrus	brain
42	chr1:223935600-223936400	Enhancers	Right Ventricle	heart
43	chr1:223935600-223936400	Enhancers	GM12878-XiMat	blood
44	chr1:223935600-223936400	Genic enhancers	Monocytes-CD14+_RO01746	blood
45	chr1:223935600-223936600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr1:223935600-223936600	Genic enhancers	Esophagus	oesophagus
47	chr1:223935600-223936800	Enhancers	Fetal Brain Male	brain
48	chr1:223935600-223937200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:223935600-223937400	Enhancers	Stomach Mucosa	stomach
50	chr1:223935800-223936400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell

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