Variant report

Variant	rs12620576
Chromosome Location	chr2:96814520-96814521
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	FOS	chr2:96814143-96814575	MCF10A-Er-Src	breast:	n/a	chr2:96814389-96814400 chr2:96814391-96814399 chr2:96814388-96814396
2	ATF2	chr2:96814194-96814818	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr2:96814346-96814622	HUVEC	blood vessel:	n/a	n/a
4	SMC3	chr2:96814149-96814724	Hela-S3	cervix:	n/a	n/a
5	USF2	chr2:96814167-96814886	H1-hESC	embryonic stem cell:	n/a	n/a
6	CREB1	chr2:96813989-96814922	GM12878	blood:	n/a	n/a
7	JUND	chr2:96814195-96814568	H1-hESC	embryonic stem cell:	n/a	chr2:96814391-96814399 chr2:96814388-96814396 chr2:96814389-96814400
8	EP300	chr2:96814059-96814564	SK-N-SH_RA	brain:	n/a	n/a
9	PAX5	chr2:96814126-96814830	GM12878	blood:	n/a	n/a
10	EP300	chr2:96814192-96814624	GM12878	blood:	n/a	n/a
11	SIN3AK20	chr2:96814076-96814571	SK-N-SH	brain:	n/a	n/a
12	EGR1	chr2:96814073-96814574	H1-hESC	embryonic stem cell:	n/a	chr2:96814268-96814281 chr2:96814453-96814463 chr2:96814536-96814546 chr2:96814531-96814544 chr2:96814527-96814549 chr2:96814534-96814544
13	KAP1	chr2:96813919-96814548	U2OS	brain:	n/a	chr2:96814389-96814398
14	JUN	chr2:96814216-96814537	H1-hESC	embryonic stem cell:	n/a	chr2:96814391-96814399 chr2:96814388-96814396
15	MAFK	chr2:96814224-96814536	H1-hESC	embryonic stem cell:	n/a	chr2:96814389-96814399
16	CEBPB	chr2:96814061-96814742	Hela-S3	cervix:	n/a	n/a
17	JUN	chr2:96814045-96814947	K562	blood:	n/a	chr2:96814391-96814399 chr2:96814388-96814396
18	TCF12	chr2:96814088-96814639	GM12878	blood:	n/a	n/a
19	ESRRA	chr2:96807401-96815327	GM12878	blood:	n/a	chr2:96814549-96814568 chr2:96812831-96812844 chr2:96814530-96814543 chr2:96808836-96808848 chr2:96812889-96812902
20	RCOR1	chr2:96814022-96814683	GM12878	blood:	n/a	n/a
21	TBP	chr2:96814027-96814622	GM12878	blood:	n/a	n/a
22	POLR2A	chr2:96813778-96814538	GM12892	blood:	n/a	n/a
23	SMARCC1	chr2:96813402-96815037	Hela-S3	cervix:	n/a	chr2:96814390-96814399
24	JUN	chr2:96814196-96814674	K562	blood:	n/a	chr2:96814391-96814399 chr2:96814388-96814396
25	POLR2A	chr2:96814078-96814716	GM12878	blood:	n/a	n/a
26	RFX5	chr2:96814153-96814720	GM12878	blood:	n/a	n/a
27	CREB1	chr2:96814009-96814928	H1-hESC	embryonic stem cell:	n/a	n/a
28	ELF1	chr2:96814062-96814976	GM12878	blood:	n/a	n/a
29	MAZ	chr2:96814064-96814974	Hela-S3	cervix:	n/a	chr2:96814921-96814930 chr2:96814534-96814544
30	PAX5	chr2:96814133-96814687	GM12878	blood:	n/a	n/a
31	EP300	chr2:96813919-96814831	SK-N-SH	brain:	n/a	chr2:96813968-96813982
32	MAZ	chr2:96813396-96814820	IMR90	lung:	n/a	chr2:96814534-96814544
33	POLR2A	chr2:96813607-96814710	GM19193	blood:	n/a	n/a
34	POLR2A	chr2:96813354-96814609	GM12878	blood:	n/a	n/a
35	BATF	chr2:96814186-96814575	GM12878	blood:	n/a	chr2:96814388-96814398
36	CREB1	chr2:96814066-96814886	H1-hESC	embryonic stem cell:	n/a	n/a
37	USF1	chr2:96814433-96814838	H1-hESC	embryonic stem cell:	n/a	n/a
38	FOS	chr2:96814195-96814563	HUVEC	blood vessel:	n/a	chr2:96814389-96814400 chr2:96814391-96814399 chr2:96814388-96814396
39	EP300	chr2:96811760-96815004	SK-N-SH	brain:	n/a	chr2:96813968-96813982 chr2:96812145-96812161 chr2:96812146-96812162
40	STAT1	chr2:96814212-96814749	GM12878	blood:	n/a	n/a
41	POLR2A	chr2:96813968-96814764	H1-neurons	neurons:	n/a	n/a
42	ZEB1	chr2:96814078-96814971	GM12878	blood:	n/a	chr2:96814545-96814554
43	PML	chr2:96806496-96814786	GM12878	blood:	n/a	chr2:96814389-96814398
44	EGR1	chr2:96814201-96814607	GM12878	blood:	n/a	chr2:96814268-96814281 chr2:96814453-96814463 chr2:96814536-96814546 chr2:96814531-96814544 chr2:96814527-96814549 chr2:96814534-96814544
45	TCF3	chr2:96814148-96814916	GM12878	blood:	n/a	n/a
46	POLR2A	chr2:96802923-96814679	GM12891	blood:	n/a	n/a
47	MAX	chr2:96814064-96815020	Hela-S3	cervix:	n/a	chr2:96814921-96814930 chr2:96814534-96814544
48	FOS	chr2:96814165-96814582	MCF10A-Er-Src	breast:	n/a	chr2:96814389-96814400 chr2:96814391-96814399 chr2:96814388-96814396
49	EP300	chr2:96813277-96815068	GM12878	blood:	n/a	chr2:96813968-96813982
50	POLR2A	chr2:96814079-96814707	GM19099	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:96813186..96815760-chr2:96873244..96875582,3	MCF-7	breast:
2	chr2:96812916..96814521-chr2:96834826..96836596,2	K562	blood:
3	chr2:96814366..96815909-chr2:96816931..96819654,2	K562	blood:

Variant related genes	Relation type
ENSG00000228873	TF binding region
DUSP2	TF binding region
ENSG00000084090	Chromatin interaction
ENSG00000204685	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12611936	1.00[AMR][1000 genomes]
rs12612136	1.00[AMR][1000 genomes]
rs12614113	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12614623	1.00[AMR][1000 genomes]
rs12616326	1.00[AMR][1000 genomes]
rs12619114	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12619490	1.00[AMR][1000 genomes]
rs12619573	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12620768	1.00[AMR][1000 genomes]
rs12621163	1.00[AMR][1000 genomes]
rs12621619	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12621688	1.00[AMR][1000 genomes]
rs2276647	1.00[AMR][1000 genomes]
rs2290908	1.00[AMR][1000 genomes]
rs3813659	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3813660	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57319731	1.00[AMR][1000 genomes]
rs57367779	1.00[AMR][1000 genomes]
rs57477571	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58132887	1.00[AMR][1000 genomes]
rs59168739	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs59525841	1.00[AMR][1000 genomes]
rs59621486	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59911784	1.00[AMR][1000 genomes]
rs60013962	1.00[AMR][1000 genomes]
rs60020980	1.00[AMR][1000 genomes]
rs60596893	1.00[AMR][1000 genomes]
rs60893927	1.00[AMR][1000 genomes]
rs61096003	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1840487	chr2:96582807-96836512	Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv874673	chr2:96647856-96825363	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	esv1825266	chr2:96704118-96830753	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1004129	chr2:96738585-96825363	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
6	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
7	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
8	nsv874675	chr2:96741944-96825363	Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
9	nsv874676	chr2:96753149-96825363	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
10	esv1819594	chr2:96755038-96833480	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
11	nsv1008495	chr2:96755070-96825363	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
12	nsv1002392	chr2:96756289-96815149	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
13	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
14	nsv1004977	chr2:96757107-96819188	Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
15	nsv1015000	chr2:96757107-96825363	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
16	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
17	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
18	nsv1007132	chr2:96767204-96829489	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96810000-96815000	Enhancers	Fetal Heart	heart
2	chr2:96810400-96815000	Enhancers	Fetal Lung	lung
3	chr2:96811200-96814600	Enhancers	Spleen	Spleen
4	chr2:96811200-96814800	Enhancers	Lung	lung
5	chr2:96811200-96815000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:96811200-96815000	Enhancers	NH-A	brain
7	chr2:96811200-96815200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:96811400-96814600	Enhancers	Osteobl	bone
9	chr2:96811400-96814800	Flanking Active TSS	Fetal Thymus	thymus
10	chr2:96811400-96815000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
11	chr2:96811400-96815200	Flanking Active TSS	Hela-S3	cervix
12	chr2:96811600-96814600	Enhancers	Left Ventricle	heart
13	chr2:96811600-96814600	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr2:96811600-96815000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:96811600-96815000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
16	chr2:96811600-96815000	Bivalent Enhancer	Fetal Muscle Leg	muscle
17	chr2:96811600-96815000	Enhancers	Right Ventricle	heart
18	chr2:96811600-96815000	Enhancers	HMEC	breast
19	chr2:96811600-96815200	Enhancers	Fetal Stomach	stomach
20	chr2:96811800-96814800	Enhancers	Adipose Nuclei	Adipose
21	chr2:96811800-96815000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr2:96811800-96815200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr2:96812200-96815000	Enhancers	Rectal Mucosa Donor 29	rectum
24	chr2:96812200-96815200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr2:96812400-96815000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr2:96812400-96815000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
27	chr2:96812400-96815000	Flanking Active TSS	Thymus	Thymus
28	chr2:96812400-96815200	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr2:96812400-96815200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:96812400-96815400	Enhancers	Primary B cells from cord blood	blood
31	chr2:96812600-96815000	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr2:96812600-96815000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:96812600-96815000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr2:96812600-96815200	Enhancers	NHEK	skin
35	chr2:96812600-96815400	Enhancers	Primary hematopoietic stem cells	blood
36	chr2:96812800-96814600	Weak transcription	Esophagus	oesophagus
37	chr2:96812800-96815400	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr2:96813000-96815000	Enhancers	Fetal Intestine Large	intestine
39	chr2:96813000-96815000	Enhancers	Dnd41	blood
40	chr2:96813000-96815200	Enhancers	Primary T cells from cord blood	blood
41	chr2:96813000-96815400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr2:96813200-96815000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
43	chr2:96813400-96814600	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr2:96813400-96814600	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr2:96813400-96815000	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr2:96813600-96814800	Enhancers	Stomach Smooth Muscle	stomach
47	chr2:96813600-96814800	Flanking Active TSS	GM12878-XiMat	blood
48	chr2:96813600-96815000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:96813600-96815000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr2:96813600-96822000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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