Variant report

Variant	rs7579125
Chromosome Location	chr2:20649490-20649491
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:119)
CpG islands
(count:61)
Chromatin interactive
region (count:26)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:119 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:20649186-20649843	HCT-116	colon:	n/a	n/a
2	JUND	chr2:20648344-20651419	Hela-S3	cervix:	n/a	n/a
3	BRCA1	chr2:20649108-20650942	Hela-S3	cervix:	n/a	n/a
4	SIN3AK20	chr2:20649273-20650947	MCF-7	breast:	n/a	n/a
5	ZKSCAN1	chr2:20649266-20650231	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr2:20646244-20650963	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr2:20646681-20651477	A549	lung:	n/a	n/a
8	MAFK	chr2:20647808-20651095	Hela-S3	cervix:	n/a	chr2:20650104-20650114 chr2:20650108-20650119 chr2:20650107-20650118 chr2:20650107-20650118 chr2:20650103-20650118 chr2:20650105-20650114 chr2:20650106-20650120 chr2:20650103-20650119
9	POLR2A	chr2:20646043-20652533	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr2:20649290-20650994	ProgFib	skin:	n/a	n/a
11	POLR2A	chr2:20646266-20651620	HUVEC	blood vessel:	n/a	n/a
12	EP300	chr2:20649173-20650731	HepG2	liver:	n/a	n/a
13	MAFK	chr2:20649164-20651096	HepG2	liver:	n/a	chr2:20650104-20650114 chr2:20650108-20650119 chr2:20650107-20650118 chr2:20650107-20650118 chr2:20650103-20650118 chr2:20650105-20650114 chr2:20650106-20650120 chr2:20650103-20650119
14	RCOR1	chr2:20646392-20650844	HepG2	liver:	n/a	n/a
15	POLR2A	chr2:20649114-20650470	PFSK-1	brain:	n/a	n/a
16	BHLHE40	chr2:20649223-20650881	HepG2	liver:	n/a	n/a
17	ELK4	chr2:20649320-20650985	Hela-S3	cervix:	n/a	n/a
18	RAD21	chr2:20649241-20651016	IMR90	lung:	n/a	chr2:20650390-20650402
19	POLR2A	chr2:20645918-20651649	HUVEC	blood vessel:	n/a	n/a
20	NR2F2	chr2:20649066-20650550	HepG2	liver:	n/a	chr2:20650286-20650301
21	POLR2A	chr2:20646294-20651502	MCF-7	breast:	n/a	n/a
22	HEY1	chr2:20645541-20650862	HepG2	liver:	n/a	chr2:20646608-20646623
23	POLR2A	chr2:20649178-20650829	HepG2	liver:	n/a	n/a
24	POLR2A	chr2:20649228-20650648	HCT-116	colon:	n/a	n/a
25	ARID3A	chr2:20648454-20651108	HepG2	liver:	n/a	chr2:20650872-20650887
26	HDAC2	chr2:20649200-20649836	HepG2	liver:	n/a	n/a
27	MYBL2	chr2:20646154-20651084	HepG2	liver:	n/a	n/a
28	RCOR1	chr2:20649029-20651012	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr2:20646006-20652601	HepG2	liver:	n/a	n/a
30	POLR2A	chr2:20649145-20650927	PANC-1	pancreas:	n/a	n/a
31	ELF1	chr2:20649133-20650534	A549	lung:	n/a	n/a
32	POLR2A	chr2:20645948-20651806	HUVEC	blood vessel:	n/a	n/a
33	POLR2A	chr2:20649149-20650817	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr2:20649214-20650053	GM12892	blood:	n/a	n/a
35	FOXA2	chr2:20649198-20649795	HepG2	liver:	n/a	n/a
36	POLR2A	chr2:20645989-20652401	IMR90	lung:	n/a	n/a
37	RAD21	chr2:20649255-20651114	HepG2	liver:	n/a	chr2:20650390-20650402
38	EP300	chr2:20649310-20651010	Hela-S3	cervix:	n/a	n/a
39	MBD4	chr2:20646527-20651011	HepG2	liver:	n/a	n/a
40	GATA2	chr2:20649313-20651089	HUVEC	blood vessel:	n/a	chr2:20649746-20649758 chr2:20649746-20649760
41	FOXA1	chr2:20649419-20649797	HepG2	liver:	n/a	n/a
42	FOXA1	chr2:20649231-20649845	HepG2	liver:	n/a	n/a
43	JUND	chr2:20649204-20650773	HepG2	liver:	n/a	n/a
44	SMC3	chr2:20648675-20650889	HepG2	liver:	n/a	n/a
45	POLR2A	chr2:20649136-20650369	GM12892	blood:	n/a	n/a
46	MAX	chr2:20649202-20650991	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr2:20645976-20650968	Hela-S3	cervix:	n/a	n/a
48	SIN3AK20	chr2:20649225-20650462	A549	lung:	n/a	n/a
49	TBP	chr2:20648355-20650973	Hela-S3	cervix:	n/a	n/a
50	TCF12	chr2:20649329-20651408	A549	lung:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:20649480-20649530	HPAEpiC	pulmonary alveolar:	n/a
2	chr2:20649480-20649530	Jurkat	blood:	n/a
3	chr2:20649480-20649530	T-47D	breast:	n/a
4	chr2:20649480-20649530	BE2_C	brain:	n/a
5	chr2:20649480-20649530	HIPEpiC	eye:	n/a
6	chr2:20649480-20649530	NHDF-neo	bronchial:	n/a
7	chr2:20649480-20649530	GM12878	blood:	n/a
8	chr2:20649480-20649530	SAEC	small airway:	n/a
9	chr2:20649480-20649530	ProgFib	skin:	n/a
10	chr2:20649480-20649530	SK-N-SH	brain:	n/a
11	chr2:20649480-20649530	SK-N-MC	brain:	n/a
12	chr2:20649480-20649530	NT2-D1	testis:	n/a
13	chr2:20649480-20649530	MCF10A-Er-Src	breast:	n/a
14	chr2:20649480-20649530	HUVEC	blood vessel:	n/a
15	chr2:20649480-20649530	HCM	heart:	n/a
16	chr2:20649480-20649530	GM06990	blood:	n/a
17	chr2:20649480-20649530	SKMC	muscle:	n/a
18	chr2:20649480-20649530	HL-60	blood:	n/a
19	chr2:20649480-20649530	AG09309	skin:	n/a
20	chr2:20649480-20649530	AG09319	gingival:	n/a
21	chr2:20649480-20649530	PFSK-1	brain:	n/a
22	chr2:20649480-20649530	HRPEpiC	eye:	n/a
23	chr2:20649480-20649530	Caco-2	colon:	n/a
24	chr2:20649480-20649530	AG04449	skin:	fetal
25	chr2:20649480-20649530	AG10803	skin:	n/a
26	chr2:20649480-20649530	HAEpiC	amniotic membrane:	n/a
27	chr2:20649480-20649530	CMK	blood:	n/a
28	chr2:20649480-20649530	HepG2	liver:	n/a
29	chr2:20649480-20649530	Hela-S3	cervix:	n/a
30	chr2:20649480-20649530	GM12891	blood:	n/a
31	chr2:20649480-20649530	HEEpiC	esophagus:	n/a
32	chr2:20649480-20649530	HRCEpiC	kidney:	n/a
33	chr2:20649480-20649530	A549	lung:	n/a
34	chr2:20649480-20649530	IMR90	lung:	fetal
35	chr2:20649480-20649530	BJ	skin:	n/a
36	chr2:20649480-20649530	Hepatocyte	liver:	n/a
37	chr2:20649480-20649530	HMEC	breast:	n/a
38	chr2:20649480-20649530	GM19239	blood:	n/a
39	chr2:20649480-20649530	HCF	heart:	n/a
40	chr2:20649480-20649530	ECC-1	luminal epithelium:	n/a
41	chr2:20649480-20649530	PrEC	prostate:	n/a
42	chr2:20649480-20649530	H1-hESC	embryonic stem cell:	embryo
43	chr2:20649480-20649530	HNPCEpiC	eye:	n/a
44	chr2:20649480-20649530	RPTEC	kidney:	n/a
45	chr2:20649480-20649530	ovcar-3	ovarian:	n/a
46	chr2:20649480-20649530	AoSMC	blood vessel:	n/a
47	chr2:20649480-20649530	NH-A	brain:	n/a
48	chr2:20649480-20649530	MCF-7	breast:	n/a
49	chr2:20649480-20649530	AG04450	lung:	fetal
50	chr2:20649480-20649530	HCT-116	colon:	n/a

(count:26 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20582061..20584787-chr2:20647277..20649666,2	MCF-7	breast:
2	chr2:20633992..20655025-chr2:20829429..20854651,127	MCF-7	breast:
3	chr2:20648813..20650365-chr8:143807958..143810608,2	MCF-7	breast:
4	chr2:20646857..20649701-chr2:20702827..20704331,2	K562	blood:
5	chr2:20647398..20650409-chr2:20654175..20656821,4	K562	blood:
6	chr2:20424066..20426931-chr2:20646792..20649592,2	MCF-7	breast:
7	chr2:20640108..20658716-chr2:20812153..20855311,258	MCF-7	breast:
8	chr2:20598069..20599864-chr2:20647082..20649646,2	MCF-7	breast:
9	chr2:20644186..20651576-chr2:20790196..20799394,18	MCF-7	breast:
10	chr2:11671004..11673308-chr2:20648459..20650037,2	MCF-7	breast:
11	chr2:20647607..20649619-chr4:103748419..103749985,2	MCF-7	breast:
12	chr2:20643596..20652981-chr2:20820571..20828990,20	MCF-7	breast:
13	chr2:20648875..20651258-chr7:86847173..86848866,2	MCF-7	breast:
14	chr2:20592640..20602218-chr2:20644635..20652468,15	MCF-7	breast:
15	chr2:20647080..20649987-chr2:27272850..27275008,2	MCF-7	breast:
16	chr2:20645526..20651779-chr2:20782666..20787622,12	MCF-7	breast:
17	chr2:20583426..20586249-chr2:20648577..20650725,2	MCF-7	breast:
18	chr2:20648478..20650764-chr2:20800436..20802695,3	MCF-7	breast:
19	chr2:20646900..20649686-chr2:20739028..20740892,2	MCF-7	breast:
20	chr2:20647900..20649947-chr2:20748002..20750388,3	MCF-7	breast:
21	chr2:8821242..8823480-chr2:20647552..20650236,2	MCF-7	breast:
22	chr2:20647678..20650094-chr2:20830839..20832383,2	K562	blood:
23	chr2:20645423..20650748-chr2:20698837..20705480,9	MCF-7	breast:
24	chr2:20647548..20649873-chr2:20806616..20809120,2	MCF-7	breast:
25	chr2:20644797..20655251-chr2:20787626..20802274,53	MCF-7	breast:
26	chr2:20548847..20552407-chr2:20645405..20649585,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000228950	TF binding region
ENSG00000228950	CpG island
ENSG00000115884	Chromatin interaction
ENSG00000253806	Chromatin interaction
ENSG00000212171	Chromatin interaction
ENSG00000227047	Chromatin interaction
ENSG00000130193	Chromatin interaction
ENSG00000269976	Chromatin interaction
ENSG00000235092	Chromatin interaction
ENSG00000232800	Chromatin interaction
ENSG00000115738	Chromatin interaction
ENSG00000246560	Chromatin interaction
ENSG00000200397	Chromatin interaction
ENSG00000109332	Chromatin interaction
ENSG00000231636	Chromatin interaction
ENSG00000084693	Chromatin interaction
ENSG00000055917	Chromatin interaction
ENSG00000253741	Chromatin interaction
ENSG00000118960	Chromatin interaction
ENSG00000231948	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs58365598	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73221992	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[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	nsv455830	chr2:20621404-20659862	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv581166	chr2:20621404-20659862	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
3	nsv873717	chr2:20625174-20756900	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
4	nsv873718	chr2:20627875-20752152	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv873719	chr2:20628882-20756900	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
6	nsv833537	chr2:20630092-20826816	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	nsv873720	chr2:20645835-20756900	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
8	nsv873721	chr2:20645835-20759789	Enhancers Bivalent Enhancer Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20643600-20650000	Active TSS	Right Atrium	heart
2	chr2:20644600-20650000	Active TSS	Psoas Muscle	Psoas
3	chr2:20645000-20650600	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr2:20645600-20650000	Active TSS	Brain Angular Gyrus	brain
5	chr2:20646000-20649600	Active TSS	HSMMtube	muscle
6	chr2:20646000-20649800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
7	chr2:20646000-20650000	Active TSS	Ovary	ovary
8	chr2:20646000-20650200	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr2:20647200-20649600	Transcr. at gene 5' and 3'	HUVEC	blood vessel
10	chr2:20647200-20649800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr2:20647200-20649800	Transcr. at gene 5' and 3'	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:20647200-20649800	Transcr. at gene 5' and 3'	A549	lung
13	chr2:20647400-20649600	Transcr. at gene 5' and 3'	Colon Smooth Muscle	Colon
14	chr2:20647400-20649600	Transcr. at gene 5' and 3'	Rectal Smooth Muscle	rectum
15	chr2:20647400-20649800	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:20647400-20649800	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland
17	chr2:20647600-20649600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:20647600-20649800	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
19	chr2:20648000-20649600	Bivalent/Poised TSS	Thymus	Thymus
20	chr2:20648000-20649800	Flanking Active TSS	Brain Germinal Matrix	brain
21	chr2:20648000-20649800	Active TSS	Brain Substantia Nigra	brain
22	chr2:20648000-20650000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:20648000-20650200	Active TSS	Breast Myoepithelial Primary Cells	Breast
24	chr2:20648200-20650000	Active TSS	Duodenum Mucosa	Duodenum
25	chr2:20648200-20650200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:20648400-20649600	Flanking Active TSS	Fetal Lung	lung
27	chr2:20648400-20650000	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
28	chr2:20648600-20649600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:20648600-20649600	Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr2:20648600-20650000	Weak transcription	Esophagus	oesophagus
31	chr2:20648600-20650000	Active TSS	Fetal Muscle Trunk	muscle
32	chr2:20648600-20650200	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
33	chr2:20648600-20650200	Active TSS	Colonic Mucosa	Colon
34	chr2:20648600-20650200	Active TSS	Lung	lung
35	chr2:20648600-20650800	Active TSS	Right Ventricle	heart
36	chr2:20648600-20651000	Active TSS	Aorta	Aorta
37	chr2:20648800-20649800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:20648800-20649800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr2:20648800-20649800	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr2:20648800-20650000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:20648800-20650000	Flanking Active TSS	Fetal Brain Male	brain
42	chr2:20648800-20650200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr2:20648800-20650400	Active TSS	Rectal Mucosa Donor 29	rectum
44	chr2:20648800-20650600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr2:20648800-20650600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr2:20649000-20649600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr2:20649000-20649600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr2:20649000-20649600	Flanking Active TSS	Fetal Kidney	kidney
49	chr2:20649000-20649600	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr2:20649000-20649800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell

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