Variant report

Variant	rs1727528
Chromosome Location	chr2:54557576-54557577
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	ELF1	chr2:54557565-54558255	MCF-7	breast:	n/a	n/a
2	POLR2A	chr2:54557372-54558079	H1-hESC	embryonic stem cell:	n/a	n/a
3	HDAC2	chr2:54557569-54558202	HepG2	liver:	n/a	n/a
4	HA-E2F1	chr2:54557360-54558286	MCF-7	breast:	n/a	chr2:54557944-54557953 chr2:54557625-54557637 chr2:54557572-54557581
5	MAX	chr2:54557355-54558165	H1-hESC	embryonic stem cell:	n/a	chr2:54557878-54557888 chr2:54557968-54557977
6	POLR2A	chr2:54557562-54558147	HUVEC	blood vessel:	n/a	n/a
7	ZNF263	chr2:54557381-54558308	HEK293-T-REx	kidney:	n/a	chr2:54558114-54558135
8	TCF12	chr2:54557319-54558450	A549	lung:	n/a	n/a
9	MAX	chr2:54557354-54558305	SK-N-SH	brain:	n/a	chr2:54557878-54557888 chr2:54557968-54557977
10	NRF1	chr2:54557015-54558431	SK-N-SH	brain:	n/a	chr2:54557945-54557954 chr2:54557943-54557957 chr2:54557940-54557954 chr2:54557943-54557954 chr2:54557943-54557954
11	RFX5	chr2:54556901-54558196	HepG2	liver:	n/a	chr2:54558000-54558014 chr2:54557573-54557582 chr2:54557997-54558013 chr2:54557998-54558012
12	ZNF143	chr2:54557478-54558244	H1-hESC	embryonic stem cell:	n/a	n/a
13	MAX	chr2:54557379-54558131	H1-hESC	embryonic stem cell:	n/a	chr2:54557878-54557888 chr2:54557968-54557977
14	REST	chr2:54557381-54558386	A549	lung:	n/a	n/a
15	JUND	chr2:54557352-54558001	H1-hESC	embryonic stem cell:	n/a	n/a
16	E2F6	chr2:54557171-54558231	H1-hESC	embryonic stem cell:	n/a	chr2:54557944-54557953 chr2:54557625-54557637 chr2:54557572-54557581
17	GATA2	chr2:54557418-54558418	SH-SY5Y	brain:	n/a	chr2:54558124-54558138
18	FOXA1	chr2:54557553-54558169	HepG2	liver:	n/a	n/a
19	MAX	chr2:54557515-54558194	HepG2	liver:	n/a	chr2:54557878-54557888 chr2:54557968-54557977
20	RCOR1	chr2:54557310-54558194	K562	blood:	n/a	n/a
21	MAX	chr2:54557216-54558378	A549	lung:	n/a	chr2:54557878-54557888 chr2:54557968-54557977
22	MXI1	chr2:54556371-54559071	SK-N-SH	brain:	n/a	n/a
23	MAZ	chr2:54556493-54559239	IMR90	lung:	n/a	chr2:54557878-54557888 chr2:54557968-54557977
24	ELF1	chr2:54557538-54558253	GM12878	blood:	n/a	n/a
25	JUND	chr2:54557490-54558201	K562	blood:	n/a	n/a
26	POLR2A	chr2:54557517-54558260	ProgFib	skin:	n/a	n/a
27	POLR2A	chr2:54557557-54558292	ECC-1	luminal epithelium:	n/a	n/a
28	POLR2A	chr2:54557245-54558276	H1-hESC	embryonic stem cell:	n/a	n/a
29	ARID3A	chr2:54557555-54557779	K562	blood:	n/a	n/a
30	POLR2A	chr2:54557502-54558301	Gliobla	brain:	n/a	n/a
31	MAX	chr2:54557187-54558242	ECC-1	luminal epithelium:	n/a	chr2:54557878-54557888 chr2:54557968-54557977
32	GATA1	chr2:54557448-54558290	PBDE	blood:	n/a	n/a
33	KAP1	chr2:54556995-54558316	HEK293	kidney:	n/a	n/a
34	TCF7L2	chr2:54557520-54558163	HCT-116	colon:	n/a	n/a
35	TEAD4	chr2:54557524-54558236	K562	blood:	n/a	n/a
36	POLR2A	chr2:54557415-54558223	SK-N-MC	brain:	n/a	n/a
37	MAX	chr2:54557357-54558271	MCF-7	breast:	n/a	chr2:54557878-54557888 chr2:54557968-54557977
38	TBP	chr2:54557501-54558042	K562	blood:	n/a	n/a
39	TAF1	chr2:54557501-54558064	H1-hESC	embryonic stem cell:	n/a	n/a
40	E2F6	chr2:54557455-54557995	K562	blood:	n/a	chr2:54557944-54557953 chr2:54557625-54557637 chr2:54557572-54557581
41	RAD21	chr2:54557276-54558357	SK-N-SH_RA	brain:	n/a	n/a
42	SIN3AK20	chr2:54557552-54558124	A549	lung:	n/a	n/a
43	MXI1	chr2:54557556-54558264	HepG2	liver:	n/a	n/a
44	MYC	chr2:54557539-54558148	K562	blood:	n/a	chr2:54557878-54557888 chr2:54557968-54557977
45	TBP	chr2:54557405-54558045	H1-hESC	embryonic stem cell:	n/a	n/a
46	TAF1	chr2:54557440-54558280	ECC-1	luminal epithelium:	n/a	n/a
47	MAZ	chr2:54557366-54558222	K562	blood:	n/a	chr2:54557878-54557888 chr2:54557968-54557977
48	MAX	chr2:54557252-54558390	HCT-116	colon:	n/a	chr2:54557878-54557888 chr2:54557968-54557977
49	GATA3	chr2:54557434-54558506	A549	lung:	n/a	n/a
50	TCF7L2	chr2:54557556-54558028	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54341307..54344135-chr2:54557168..54559182,2	K562	blood:

Variant related genes	Relation type
C2orf73	TF binding region
ENSG00000170634	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1385275	0.92[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1385276	0.92[CEU][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1682138	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1682139	0.96[CEU][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17268409	0.81[JPT][hapmap]
rs1727530	0.96[CEU][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs1727532	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2204628	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs843632	0.82[GIH][hapmap];0.80[JPT][hapmap]

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	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv532512	chr2:54453210-54630755	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1004632	chr2:54469283-54590480	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	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	chr2:54556800-54557600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr2:54556800-54557600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr2:54556800-54557600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:54556800-54557600	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr2:54556800-54557600	Flanking Active TSS	Fetal Heart	heart
6	chr2:54556800-54557800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:54556800-54557800	Flanking Active TSS	HepG2	liver
8	chr2:54556800-54557800	Flanking Active TSS	NHEK	skin
9	chr2:54556800-54557800	Flanking Active TSS	Osteobl	bone
10	chr2:54556800-54558400	Active TSS	Brain Substantia Nigra	brain
11	chr2:54556800-54558600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
12	chr2:54557000-54557600	Flanking Active TSS	Fetal Lung	lung
13	chr2:54557000-54557600	Flanking Active TSS	Fetal Muscle Leg	muscle
14	chr2:54557000-54557600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
15	chr2:54557000-54557600	Flanking Active TSS	Stomach Smooth Muscle	stomach
16	chr2:54557000-54557800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:54557000-54557800	Flanking Active TSS	NH-A	brain
18	chr2:54557000-54558200	Active TSS	Esophagus	oesophagus
19	chr2:54557000-54558200	Active TSS	HSMMtube	muscle
20	chr2:54557000-54558400	Active TSS	H1 Cell Line	embryonic stem cell
21	chr2:54557000-54558400	Active TSS	H9 Cell Line	embryonic stem cell
22	chr2:54557000-54558400	Active TSS	Aorta	Aorta
23	chr2:54557000-54558400	Active TSS	Right Ventricle	heart
24	chr2:54557000-54558600	Flanking Active TSS	Liver	Liver
25	chr2:54557000-54558800	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr2:54557000-54558800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr2:54557000-54558800	Flanking Active TSS	Duodenum Mucosa	Duodenum
28	chr2:54557000-54558800	Flanking Active TSS	Dnd41	blood
29	chr2:54557200-54557600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
30	chr2:54557200-54557600	Flanking Active TSS	Brain Germinal Matrix	brain
31	chr2:54557200-54557600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
32	chr2:54557200-54557600	Flanking Active TSS	Fetal Intestine Large	intestine
33	chr2:54557200-54557600	Active TSS	Fetal Muscle Trunk	muscle
34	chr2:54557200-54557600	Flanking Active TSS	Fetal Stomach	stomach
35	chr2:54557200-54557600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
36	chr2:54557200-54557600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
37	chr2:54557200-54557600	Active TSS	Right Atrium	heart
38	chr2:54557200-54557600	Flanking Active TSS	A549	lung
39	chr2:54557200-54557800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
40	chr2:54557200-54557800	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
41	chr2:54557200-54557800	Flanking Active TSS	K562	blood
42	chr2:54557200-54558000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr2:54557200-54558200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr2:54557200-54558200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr2:54557200-54558200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr2:54557200-54558200	Active TSS	Placenta Amnion	Placenta Amnion
47	chr2:54557200-54558200	Active TSS	Sigmoid Colon	Sigmoid Colon
48	chr2:54557200-54558400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr2:54557200-54558400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr2:54557200-54558400	Active TSS	HUES64 Cell Line	embryonic stem cell

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