Variant report

Variant	rs62136446
Chromosome Location	chr2:64246256-64246257
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	TAF1	chr2:64245855-64246833	HepG2	liver:	n/a	n/a
2	MAX	chr2:64245682-64247362	A549	lung:	n/a	chr2:64246699-64246706 chr2:64246699-64246709 chr2:64246699-64246708
3	RUNX3	chr2:64246178-64247052	GM12878	blood:	n/a	n/a
4	TAF1	chr2:64246201-64246768	K562	blood:	n/a	n/a
5	MAX	chr2:64245807-64247301	A549	lung:	n/a	chr2:64246699-64246706 chr2:64246699-64246709 chr2:64246699-64246708
6	SIN3AK20	chr2:64246232-64246500	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr2:64245521-64246856	GM15510	blood:	n/a	n/a
8	ZNF143	chr2:64246106-64247024	GM12878	blood:	n/a	n/a
9	REST	chr2:64246209-64246493	A549	lung:	n/a	n/a
10	POLR2A	chr2:64246239-64246947	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr2:64246188-64247291	SK-N-MC	brain:	n/a	n/a
12	GABPA	chr2:64246246-64246747	K562	blood:	n/a	chr2:64246659-64246673
13	POLR2A	chr2:64245738-64246926	MCF-7	breast:	n/a	n/a
14	HEY1	chr2:64245343-64247327	HepG2	liver:	n/a	chr2:64247192-64247201 chr2:64246048-64246063
15	POLR2A	chr2:64246218-64247210	HCT-116	colon:	n/a	n/a
16	POLR2A	chr2:64245750-64246943	HUVEC	blood vessel:	n/a	n/a
17	EGR1	chr2:64245981-64246675	GM12878	blood:	n/a	chr2:64246117-64246127 chr2:64246358-64246372 chr2:64246050-64246060
18	TAF1	chr2:64246195-64246878	H1-hESC	embryonic stem cell:	n/a	n/a
19	REST	chr2:64245367-64247177	H1-neurons	neurons:	n/a	chr2:64246077-64246090
20	SMARCB1	chr2:64245790-64246975	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr2:64246185-64247192	HepG2	liver:	n/a	n/a
22	POLR2A	chr2:64246171-64246531	U87	brain:	n/a	n/a
23	SPI1	chr2:64245482-64246342	GM12878	blood:	n/a	chr2:64245893-64245906 chr2:64245894-64245907
24	POLR2A	chr2:64246208-64247232	PFSK-1	brain:	n/a	n/a
25	POLR2A	chr2:64246192-64246934	HL-60	blood:	n/a	n/a
26	POLR2A	chr2:64246172-64246853	HCT-116	colon:	n/a	n/a
27	POLR2A	chr2:64245470-64247182	IMR90	lung:	n/a	n/a
28	MYC	chr2:64245334-64247267	K562	blood:	n/a	chr2:64246699-64246706 chr2:64246699-64246709 chr2:64246699-64246708
29	MAX	chr2:64246220-64246952	SK-N-SH	brain:	n/a	chr2:64246699-64246706 chr2:64246699-64246709 chr2:64246699-64246708
30	TAF1	chr2:64245466-64247022	ECC-1	luminal epithelium:	n/a	n/a
31	POLR2A	chr2:64246178-64246843	HCT-116	colon:	n/a	n/a
32	POLR2A	chr2:64245828-64247072	GM12878	blood:	n/a	n/a
33	YY1	chr2:64245782-64246752	GM12878	blood:	n/a	chr2:64246051-64246062 chr2:64246486-64246500 chr2:64246483-64246497 chr2:64245966-64245977 chr2:64246115-64246124 chr2:64246538-64246549 chr2:64246116-64246130 chr2:64246053-64246062 chr2:64246708-64246719 chr2:64246292-64246306
34	BCLAF1	chr2:64246256-64246782	GM12878	blood:	n/a	n/a
35	SMC3	chr2:64246256-64247182	Hela-S3	cervix:	n/a	n/a
36	ETS1	chr2:64246182-64246763	K562	blood:	n/a	n/a
37	MXI1	chr2:64246067-64247235	IMR90	lung:	n/a	n/a
38	YY1	chr2:64245784-64246950	HepG2	liver:	n/a	chr2:64246051-64246062 chr2:64246486-64246500 chr2:64246483-64246497 chr2:64245966-64245977 chr2:64246115-64246124 chr2:64246538-64246549 chr2:64246116-64246130 chr2:64246053-64246062 chr2:64246708-64246719 chr2:64246292-64246306
39	POLR2A	chr2:64246173-64247089	PFSK-1	brain:	n/a	n/a
40	POLR2A	chr2:64245481-64247033	MCF-7	breast:	n/a	n/a
41	TAF1	chr2:64245699-64246877	ECC-1	luminal epithelium:	n/a	n/a
42	POLR2A	chr2:64245766-64246868	H1-neurons	neurons:	n/a	n/a
43	POLR2A	chr2:64245423-64247115	Hela-S3	cervix:	n/a	n/a
44	CCNT2	chr2:64245986-64246822	K562	blood:	n/a	chr2:64245987-64245996
45	POLR2A	chr2:64245727-64246865	GM12878	blood:	n/a	n/a
46	MAX	chr2:64245746-64246932	MCF-7	breast:	n/a	chr2:64246699-64246706 chr2:64246699-64246709 chr2:64246699-64246708
47	MAZ	chr2:64245738-64247138	Hela-S3	cervix:	n/a	chr2:64246699-64246706 chr2:64246699-64246709 chr2:64246699-64246708
48	POLR2A	chr2:64246001-64246899	H1-neurons	neurons:	n/a	n/a
49	POLR2A	chr2:64245442-64247221	HepG2	liver:	n/a	n/a
50	MAX	chr2:64245758-64247011	K562	blood:	n/a	chr2:64246699-64246706 chr2:64246699-64246709 chr2:64246699-64246708

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:64245248..64247097-chr2:64369855..64371570,2	MCF-7	breast:

Variant related genes	Relation type
VPS54	TF binding region
ENSG00000225889	Chromatin interaction
ENSG00000197329	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10496104	0.91[AMR][1000 genomes]
rs11896894	0.91[AMR][1000 genomes]
rs11899693	0.91[AMR][1000 genomes]
rs17028239	0.91[AMR][1000 genomes]
rs17028316	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4277507	0.91[AMR][1000 genomes]
rs4470330	0.91[AMR][1000 genomes]
rs55977137	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56053068	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56155077	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56674285	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56978264	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57085982	0.84[AMR][1000 genomes]
rs57252448	1.00[EUR][1000 genomes]
rs57936760	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58074696	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58198691	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58297806	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58889204	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58982089	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59156176	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59335889	0.84[AMR][1000 genomes]
rs59736629	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60350159	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60847776	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61486417	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62136407	0.84[AMR][1000 genomes]
rs62136423	0.84[AMR][1000 genomes]
rs62136425	0.82[EUR][1000 genomes]
rs62136429	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62136436	0.94[EUR][1000 genomes]
rs62136447	0.94[EUR][1000 genomes]
rs62136457	0.94[EUR][1000 genomes]
rs62136458	0.94[EUR][1000 genomes]
rs62136459	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531376	chr2:64094322-64521876	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv2763643	chr2:64219887-64281337	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1013132	chr2:64235175-64631084	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64243000-64246800	Active TSS	GM12878-XiMat	blood
2	chr2:64244000-64246800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr2:64244400-64246600	Active TSS	Muscle Satellite Cultured Cells	--
4	chr2:64244400-64246600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:64244600-64246400	Active TSS	HMEC	breast
6	chr2:64244600-64246600	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr2:64244600-64246600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:64244600-64246800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr2:64244600-64246800	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr2:64244600-64246800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:64244600-64246800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr2:64244600-64246800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr2:64244600-64246800	Active TSS	Fetal Kidney	kidney
14	chr2:64244600-64246800	Active TSS	Stomach Smooth Muscle	stomach
15	chr2:64244600-64246800	Active TSS	HSMMtube	muscle
16	chr2:64244600-64246800	Active TSS	K562	blood
17	chr2:64244600-64246800	Active TSS	NHDF-Ad	bronchial
18	chr2:64244600-64246800	Active TSS	NHEK	skin
19	chr2:64244600-64246800	Active TSS	NHLF	lung
20	chr2:64244600-64247000	Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr2:64244600-64247200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr2:64244600-64247400	Active TSS	Brain Angular Gyrus	brain
23	chr2:64244800-64246600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:64244800-64246600	Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr2:64244800-64246600	Active TSS	Rectal Mucosa Donor 31	rectum
26	chr2:64244800-64246800	Active TSS	H1 Cell Line	embryonic stem cell
27	chr2:64244800-64246800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr2:64244800-64246800	Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr2:64244800-64246800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:64244800-64246800	Active TSS	Aorta	Aorta
31	chr2:64244800-64246800	Active TSS	Brain Germinal Matrix	brain
32	chr2:64244800-64246800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr2:64244800-64246800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
34	chr2:64244800-64246800	Active TSS	Fetal Brain Female	brain
35	chr2:64244800-64246800	Active TSS	Fetal Intestine Large	intestine
36	chr2:64244800-64246800	Active TSS	Fetal Intestine Small	intestine
37	chr2:64244800-64246800	Active TSS	Fetal Muscle Leg	muscle
38	chr2:64244800-64246800	Active TSS	Fetal Stomach	stomach
39	chr2:64244800-64246800	Active TSS	Left Ventricle	heart
40	chr2:64244800-64246800	Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr2:64244800-64246800	Active TSS	Skeletal Muscle Female	skeletal muscle
42	chr2:64244800-64246800	Active TSS	HSMM	muscle
43	chr2:64244800-64247000	Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr2:64244800-64247000	Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr2:64244800-64247000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr2:64244800-64247000	Active TSS	Ovary	ovary
47	chr2:64244800-64247000	Active TSS	Right Ventricle	heart
48	chr2:64244800-64247200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr2:64244800-64247200	Active TSS	Psoas Muscle	Psoas
50	chr2:64244800-64247200	Active TSS	Right Atrium	heart

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