Variant report

Variant	rs62446277
Chromosome Location	chr7:25989960-25989961
allele	A/C
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	SIN3A	chr7:25989265-25991735	H1-hESC	embryonic stem cell:	n/a	chr7:25990195-25990206 chr7:25990193-25990206 chr7:25991169-25991182 chr7:25990724-25990737 chr7:25991166-25991175 chr7:25991177-25991190 chr7:25990883-25990894
2	POLR2A	chr7:25985526-25991809	GM19099	blood:	n/a	n/a
3	WRNIP1	chr7:25989375-25989986	GM12878	blood:	n/a	n/a
4	CTCF	chr7:25989840-25990090	GM12864	blood:	n/a	n/a
5	SIN3AK20	chr7:25989901-25990600	H1-hESC	embryonic stem cell:	n/a	n/a
6	ZNF143	chr7:25989454-25990268	H1-hESC	embryonic stem cell:	n/a	chr7:25990014-25990024
7	MAX	chr7:25989822-25991418	H1-hESC	embryonic stem cell:	n/a	chr7:25990932-25990943 chr7:25991249-25991259
8	BRCA1	chr7:25989762-25990253	H1-hESC	embryonic stem cell:	n/a	chr7:25989786-25989793
9	POLR2A	chr7:25987021-25992694	HepG2	liver:	n/a	n/a
10	POLR2A	chr7:25986974-25991365	HepG2	liver:	n/a	n/a
11	CREB1	chr7:25989239-25991492	HepG2	liver:	n/a	n/a
12	POLR2A	chr7:25989708-25991441	HL-60	blood:	n/a	n/a
13	POLR2A	chr7:25989717-25990490	H1-hESC	embryonic stem cell:	n/a	n/a
14	EBF1	chr7:25989348-25990122	GM12878	blood:	n/a	chr7:25989451-25989460 chr7:25989451-25989461 chr7:25989531-25989542
15	POLR2A	chr7:25989404-25990965	K562	blood:	n/a	n/a
16	POLR2A	chr7:25986274-25991748	GM18526	blood:	n/a	n/a
17	TAF1	chr7:25989818-25990968	H1-hESC	embryonic stem cell:	n/a	n/a
18	MAX	chr7:25989202-25990609	H1-hESC	embryonic stem cell:	n/a	n/a
19	JUND	chr7:25989914-25990365	H1-hESC	embryonic stem cell:	n/a	n/a
20	YY1	chr7:25989936-25990316	H1-hESC	embryonic stem cell:	n/a	chr7:25990005-25990019 chr7:25990008-25990017 chr7:25990011-25990020 chr7:25990009-25990020
21	CHD2	chr7:25989872-25990026	K562	blood:	n/a	n/a
22	ZBTB7A	chr7:25989942-25990985	K562	blood:	n/a	chr7:25990625-25990636 chr7:25990624-25990635
23	POLR2A	chr7:25985030-25991406	GM12878	blood:	n/a	n/a
24	MAZ	chr7:25989269-25991382	K562	blood:	n/a	chr7:25990932-25990943 chr7:25991249-25991259
25	CTCF	chr7:25989900-25990050	GM12871	blood:	n/a	n/a
26	HEY1	chr7:25989723-25990971	HepG2	liver:	n/a	chr7:25990009-25990024
27	CHD2	chr7:25989308-25990034	GM12878	blood:	n/a	chr7:25989460-25989467
28	YY1	chr7:25989945-25991412	HepG2	liver:	n/a	chr7:25990005-25990019 chr7:25991311-25991320 chr7:25990683-25990697 chr7:25990008-25990017 chr7:25990671-25990685 chr7:25990011-25990020 chr7:25990009-25990020
29	POLR2A	chr7:25989181-25991421	GM19193	blood:	n/a	n/a
30	EGR1	chr7:25989886-25990097	K562	blood:	n/a	chr7:25990009-25990022 chr7:25990008-25990018
31	POLR2A	chr7:25989945-25990968	K562	blood:	n/a	n/a
32	RUNX3	chr7:25989276-25989994	GM12878	blood:	n/a	n/a
33	POLR2A	chr7:25989313-25991380	GM12892	blood:	n/a	n/a
34	BHLHE40	chr7:25989321-25991286	K562	blood:	n/a	chr7:25990931-25990944 chr7:25990933-25990942 chr7:25990933-25990942 chr7:25990932-25990941
35	JUND	chr7:25989306-25990017	K562	blood:	n/a	n/a
36	MYC	chr7:25989306-25990131	K562	blood:	n/a	n/a
37	POLR2A	chr7:25989720-25990475	H1-hESC	embryonic stem cell:	n/a	n/a
38	ELK1	chr7:25989776-25989976	K562	blood:	n/a	n/a
39	BHLHE40	chr7:25989373-25991373	HepG2	liver:	n/a	chr7:25990931-25990944 chr7:25990933-25990942 chr7:25990933-25990942 chr7:25990932-25990941
40	YY1	chr7:25989928-25990438	H1-hESC	embryonic stem cell:	n/a	chr7:25990005-25990019 chr7:25990008-25990017 chr7:25990011-25990020 chr7:25990009-25990020
41	TEAD4	chr7:25989205-25989961	K562	blood:	n/a	n/a
42	RCOR1	chr7:25989255-25991064	K562	blood:	n/a	n/a
43	ATF2	chr7:25989256-25989966	H1-hESC	embryonic stem cell:	n/a	n/a
44	MXI1	chr7:25988971-25990128	GM12878	blood:	n/a	n/a
45	ATF2	chr7:25989843-25990369	H1-hESC	embryonic stem cell:	n/a	n/a
46	MAZ	chr7:25989897-25990339	HepG2	liver:	n/a	n/a
47	TAF7	chr7:25989881-25990435	H1-hESC	embryonic stem cell:	n/a	n/a
48	ZNF143	chr7:25989330-25989968	K562	blood:	n/a	n/a
49	RAD21	chr7:25989960-25990343	H1-hESC	embryonic stem cell:	n/a	chr7:25990005-25990015
50	POLR2A	chr7:25989156-25991518	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:25932775..25935474-chr7:25989853..25992220,2	K562	blood:
2	chr7:25989265..25991851-chr7:26238825..26240746,4	MCF-7	breast:
3	chr7:25901871..25903514-chr7:25989852..25991943,2	K562	blood:
4	chr7:25989811..25992726-chr7:26096097..26097704,2	MCF-7	breast:
5	chr7:25901385..25904121-chr7:25989908..25991928,2	MCF-7	breast:
6	chr7:25952760..25954350-chr7:25989892..25992459,2	K562	blood:

Variant related genes	Relation type
MIR148A	TF binding region
ENSG00000270933	TF binding region
ENSG00000122566	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10261878	0.82[AMR][1000 genomes]
rs13231897	0.86[AFR][1000 genomes]
rs4412274	0.81[AFR][1000 genomes]
rs6461895	0.86[EUR][1000 genomes]
rs6461897	0.86[EUR][1000 genomes]
rs66892818	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67612070	0.86[EUR][1000 genomes]
rs6947509	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6953596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6966574	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6977848	0.87[AFR][1000 genomes]
rs7787943	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7810027	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016813	chr7:25405859-26150509	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
2	nsv538803	chr7:25405859-26150509	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	108 gene(s)	inside rSNPs	diseases
3	nsv606432	chr7:25988185-26223294	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
4	esv3394736	chr7:25989527-25992275	Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	90 gene(s)	inside rSNPs	diseases
5	esv3425784	chr7:25989652-25992200	Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 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	chr7:25987200-25993200	Active TSS	Pancreas	Pancrea
2	chr7:25987800-25992800	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr7:25988200-25990000	Flanking Active TSS	Liver	Liver
4	chr7:25988200-25990200	Flanking Active TSS	Duodenum Mucosa	Duodenum
5	chr7:25988400-25990200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr7:25989000-25990000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
7	chr7:25989000-25990000	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
8	chr7:25989000-25990000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr7:25989000-25990000	Flanking Active TSS	K562	blood
10	chr7:25989000-25990200	Flanking Active TSS	Fetal Thymus	thymus
11	chr7:25989000-25990200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
12	chr7:25989000-25991400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr7:25989200-25990000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
14	chr7:25989200-25990000	Flanking Active TSS	NHEK	skin
15	chr7:25989200-25990200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr7:25989200-25990400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
17	chr7:25989200-25990400	Flanking Active TSS	Colonic Mucosa	Colon
18	chr7:25989200-25991400	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr7:25989200-25991600	Active TSS	Rectal Smooth Muscle	rectum
20	chr7:25989200-25992600	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr7:25989400-25990000	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr7:25989400-25990000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr7:25989400-25990000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr7:25989400-25990000	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
25	chr7:25989400-25990000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
26	chr7:25989400-25990000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr7:25989400-25990000	Flanking Active TSS	Fetal Intestine Small	intestine
28	chr7:25989400-25990000	Flanking Active TSS	Placenta	Placenta
29	chr7:25989400-25990000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
30	chr7:25989400-25990000	Flanking Active TSS	Right Ventricle	heart
31	chr7:25989400-25990000	Flanking Active TSS	Stomach Smooth Muscle	stomach
32	chr7:25989400-25990200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
33	chr7:25989400-25990200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr7:25989400-25990200	Enhancers	Spleen	Spleen
35	chr7:25989400-25990200	Flanking Active TSS	HMEC	breast
36	chr7:25989400-25990400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
37	chr7:25989400-25990400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr7:25989400-25990400	Flanking Active TSS	Adipose Nuclei	Adipose
39	chr7:25989400-25990400	Bivalent/Poised TSS	NHDF-Ad	bronchial
40	chr7:25989400-25990600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
41	chr7:25989400-25990600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
42	chr7:25989400-25991400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr7:25989400-25991400	Active TSS	HUES64 Cell Line	embryonic stem cell
44	chr7:25989400-25991400	Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr7:25989400-25991400	Active TSS	iPS-20b Cell Line	embryonic stem cell
46	chr7:25989400-25991400	Active TSS	Gastric	stomach
47	chr7:25989400-25991600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr7:25989400-25991600	Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr7:25989400-25991600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr7:25989400-25991800	Active TSS	Fetal Kidney	kidney

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