Variant report

Variant	rs59525841
Chromosome Location	chr2:96971692-96971693
allele	A/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	CEBPB	chr2:96971193-96972008	K562	blood:	n/a	n/a
2	CHD1	chr2:96970695-96971823	H1-hESC	embryonic stem cell:	n/a	chr2:96971245-96971255 chr2:96971340-96971350
3	ARID3A	chr2:96971016-96971776	HepG2	liver:	n/a	n/a
4	MAX	chr2:96970962-96971722	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr2:96970646-96972437	K562	blood:	n/a	n/a
6	EP300	chr2:96971098-96972503	K562	blood:	n/a	chr2:96972078-96972088
7	ELK1	chr2:96970843-96971862	K562	blood:	n/a	n/a
8	GABPA	chr2:96970911-96971874	HepG2	liver:	n/a	chr2:96971310-96971317
9	ELK4	chr2:96970985-96972279	Hela-S3	cervix:	n/a	chr2:96971311-96971322
10	POLR2A	chr2:96970733-96972080	Hela-S3	cervix:	n/a	n/a
11	RELA	chr2:96970991-96971924	GM19099	blood:	n/a	n/a
12	GABPA	chr2:96970872-96971945	HL-60	blood:	n/a	chr2:96971310-96971317
13	GABPA	chr2:96971008-96971776	H1-hESC	embryonic stem cell:	n/a	chr2:96971310-96971317
14	SIN3AK20	chr2:96970896-96971783	A549	lung:	n/a	n/a
15	POLR2A	chr2:96971047-96971819	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr2:96970945-96971822	HCT-116	colon:	n/a	n/a
17	JUND	chr2:96970992-96971726	H1-hESC	embryonic stem cell:	n/a	chr2:96971338-96971347
18	POLR2A	chr2:96970673-96971937	HUVEC	blood vessel:	n/a	n/a
19	ETS1	chr2:96970925-96972036	A549	lung:	n/a	chr2:96971311-96971321 chr2:96971590-96971599 chr2:96971311-96971322 chr2:96971591-96971600
20	POLR2A	chr2:96970750-96972375	GM18505	blood:	n/a	n/a
21	TBP	chr2:96970622-96972307	HepG2	liver:	n/a	n/a
22	POLR2A	chr2:96970747-96972139	GM12892	blood:	n/a	n/a
23	GABPA	chr2:96971022-96971778	Hela-S3	cervix:	n/a	chr2:96971310-96971317
24	TEAD4	chr2:96970922-96971933	ECC-1	luminal epithelium:	n/a	n/a
25	POLR2A	chr2:96971034-96971794	GM10847	blood:	n/a	n/a
26	UBTF	chr2:96970987-96972098	K562	blood:	n/a	n/a
27	IRF1	chr2:96971025-96972184	K562	blood:	n/a	chr2:96971772-96971786 chr2:96971750-96971764 chr2:96971748-96971762 chr2:96971338-96971352 chr2:96971776-96971790
28	YY1	chr2:96971013-96971737	HCT-116	colon:	n/a	n/a
29	POLR2A	chr2:96970868-96972479	K562	blood:	n/a	n/a
30	GABPA	chr2:96970662-96972274	HL-60	blood:	n/a	chr2:96971310-96971317
31	ELF1	chr2:96970975-96971771	K562	blood:	n/a	chr2:96971314-96971323 chr2:96971313-96971322 chr2:96971313-96971324
32	SP1	chr2:96971163-96971733	GM12878	blood:	n/a	chr2:96971338-96971350 chr2:96971338-96971350 chr2:96971204-96971214 chr2:96971340-96971349 chr2:96971339-96971348 chr2:96971338-96971349 chr2:96971340-96971349
33	PML	chr2:96970903-96971775	MCF-7	breast:	n/a	chr2:96971751-96971759
34	TAF1	chr2:96971005-96971804	Hela-S3	cervix:	n/a	n/a
35	CREB1	chr2:96970652-96972234	HepG2	liver:	n/a	n/a
36	POLR2A	chr2:96970660-96972341	PFSK-1	brain:	n/a	n/a
37	ETS1	chr2:96970984-96971756	GM12878	blood:	n/a	chr2:96971311-96971321 chr2:96971590-96971599 chr2:96971311-96971322 chr2:96971591-96971600
38	SPI1	chr2:96971504-96971717	K562	blood:	n/a	chr2:96971601-96971608
39	POLR2A	chr2:96970269-96972563	PANC-1	pancreas:	n/a	n/a
40	FOXM1	chr2:96970797-96971998	GM12878	blood:	n/a	n/a
41	POLR2A	chr2:96970856-96971889	GM19193	blood:	n/a	n/a
42	POLR2A	chr2:96970750-96971894	GM12878	blood:	n/a	n/a
43	HDAC2	chr2:96970925-96971837	HepG2	liver:	n/a	chr2:96971285-96971299
44	GABPA	chr2:96970950-96971715	H1-hESC	embryonic stem cell:	n/a	chr2:96971310-96971317
45	YY1	chr2:96971005-96971701	SK-N-SH_RA	brain:	n/a	n/a
46	SRF	chr2:96970983-96971862	ECC-1	luminal epithelium:	n/a	chr2:96971073-96971083
47	GTF2F1	chr2:96970770-96972122	K562	blood:	n/a	n/a
48	TBP	chr2:96970982-96971906	Hela-S3	cervix:	n/a	n/a
49	MAX	chr2:96970983-96972068	SK-N-SH	brain:	n/a	n/a
50	ZC3H11A	chr2:96970865-96972581	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:96930148..96938607-chr2:96966008..96973188,21	MCF-7	breast:
2	chr2:96968224..96973301-chr2:96983171..96988936,6	MCF-7	breast:
3	chr2:96967785..96972096-chr2:96987875..96991841,5	K562	blood:
4	chr2:96969192..96974477-chr2:96999948..97003661,14	K562	blood:
5	chr2:96872463..96876007-chr2:96971318..96973774,3	MCF-7	breast:
6	chr2:96946287..96947910-chr2:96970325..96972157,2	MCF-7	breast:
7	chr15:65117834..65118481-chr2:96971362..96971901,2	Hela-S3	cervix:
8	chr2:96968671..96973165-chr2:96996066..97004511,14	MCF-7	breast:
9	chr2:96969674..96973937-chr2:96983543..96988332,6	MCF-7	breast:
10	chr2:96971195..96973076-chr2:96991103..96992730,2	MCF-7	breast:
11	chr2:96969876..96972169-chr2:97534530..97536512,2	MCF-7	breast:
12	chr2:96970144..96972526-chr2:96999842..97002907,4	MCF-7	breast:
13	chr19:12902289..12902838-chr2:96971340..96971921,2	NB4	blood:
14	chr2:96869427..96871846-chr2:96971541..96973086,2	K562	blood:
15	chr2:96928652..96934635-chr2:96966746..96973769,11	K562	blood:
16	chr11:65190164..65190772-chr2:96971401..96972046,2	Hela-S3	cervix:
17	chr2:96925245..96927615-chr2:96969806..96971741,2	MCF-7	breast:
18	chr2:96970733..96972591-chr2:97173678..97175597,2	MCF-7	breast:
19	chr2:96971094..96971792-chr5:40834950..40835771,2	Hela-S3	cervix:
20	chr2:96971462..96972991-chr2:97010337..97011869,2	MCF-7	breast:
21	chr2:96930218..96933448-chr2:96968870..96972894,6	MCF-7	breast:

Variant related genes	Relation type
SNRNP200	TF binding region
ENSG00000084090	Chromatin interaction
ENSG00000144021	Chromatin interaction
ENSG00000230747	Chromatin interaction
ENSG00000168758	Chromatin interaction
ENSG00000121152	Chromatin interaction
ENSG00000135956	Chromatin interaction
ENSG00000198885	Chromatin interaction
ENSG00000171223	Chromatin interaction
ENSG00000204685	Chromatin interaction
ENSG00000145592	Chromatin interaction
ENSG00000140451	Chromatin interaction
ENSG00000245532	Chromatin interaction
ENSG00000163121	Chromatin interaction
ENSG00000144028	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12611936	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12612136	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12614113	1.00[AMR][1000 genomes]
rs12614623	1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12616326	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12619114	1.00[AMR][1000 genomes]
rs12619490	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12619573	1.00[AMR][1000 genomes]
rs12619919	1.00[AMR][1000 genomes]
rs12620576	1.00[AMR][1000 genomes]
rs12620768	1.00[AMR][1000 genomes]
rs12621163	1.00[AMR][1000 genomes]
rs12621619	1.00[AMR][1000 genomes]
rs12621688	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2276647	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2290908	1.00[AMR][1000 genomes]
rs3813659	1.00[AMR][1000 genomes]
rs3813660	1.00[AMR][1000 genomes]
rs56742757	0.96[ASN][1000 genomes]
rs57213829	1.00[AMR][1000 genomes]
rs57248244	1.00[ASN][1000 genomes]
rs57319731	1.00[AMR][1000 genomes]
rs57367779	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57477571	1.00[AMR][1000 genomes]
rs58132887	1.00[AMR][1000 genomes]
rs58152078	1.00[AMR][1000 genomes]
rs59168739	1.00[AMR][1000 genomes]
rs59621486	1.00[AMR][1000 genomes]
rs59911784	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59939559	1.00[AMR][1000 genomes]
rs60013962	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60020980	1.00[AMR][1000 genomes]
rs60302421	1.00[AMR][1000 genomes]
rs60596893	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60893927	1.00[AMR][1000 genomes]
rs61096003	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	nsv834305	chr2:96848898-97019476	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	nsv874679	chr2:96860971-97184160	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
9	nsv508155	chr2:96934695-97138302	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 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	chr2:96970000-96972000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr2:96970200-96972000	Active TSS	HUES48 Cell Line	embryonic stem cell
3	chr2:96970200-96972400	Active TSS	H1 Cell Line	embryonic stem cell
4	chr2:96970200-96972600	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr2:96970400-96972000	Active TSS	H9 Cell Line	embryonic stem cell
6	chr2:96970400-96972000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:96970400-96972000	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr2:96970400-96972200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:96970600-96971800	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr2:96970600-96971800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
11	chr2:96970600-96971800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:96970600-96971800	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr2:96970600-96971800	Active TSS	Brain Cingulate Gyrus	brain
14	chr2:96970600-96971800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr2:96970600-96971800	Active TSS	Esophagus	oesophagus
16	chr2:96970600-96971800	Active TSS	Fetal Intestine Large	intestine
17	chr2:96970600-96971800	Active TSS	Fetal Intestine Small	intestine
18	chr2:96970600-96971800	Active TSS	Fetal Stomach	stomach
19	chr2:96970600-96971800	Active TSS	Gastric	stomach
20	chr2:96970600-96971800	Active TSS	Left Ventricle	heart
21	chr2:96970600-96971800	Active TSS	Lung	lung
22	chr2:96970600-96971800	Active TSS	Pancreas	Pancrea
23	chr2:96970600-96971800	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr2:96970600-96971800	Active TSS	Right Ventricle	heart
25	chr2:96970600-96972000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr2:96970600-96972000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:96970600-96972000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:96970600-96972000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr2:96970600-96972000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr2:96970600-96972000	Active TSS	HUES64 Cell Line	embryonic stem cell
31	chr2:96970600-96972000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:96970600-96972000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
33	chr2:96970600-96972000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
34	chr2:96970600-96972000	Active TSS	Aorta	Aorta
35	chr2:96970600-96972000	Active TSS	Colonic Mucosa	Colon
36	chr2:96970600-96972000	Active TSS	Ovary	ovary
37	chr2:96970600-96972000	Active TSS	Psoas Muscle	Psoas
38	chr2:96970600-96972000	Active TSS	A549	lung
39	chr2:96970600-96972000	Bivalent/Poised TSS	HepG2	liver
40	chr2:96970600-96972000	Active TSS	K562	blood
41	chr2:96970600-96972200	Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr2:96970600-96972200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr2:96970600-96972200	Active TSS	GM12878-XiMat	blood
44	chr2:96970600-96972400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr2:96970600-96972400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr2:96970800-96971800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr2:96970800-96971800	Active TSS	Primary T helper naive cells from peripheral blood	blood
48	chr2:96970800-96971800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr2:96970800-96971800	Active TSS	Primary T killer memory cells from peripheral blood	blood
50	chr2:96970800-96971800	Active TSS	Brain Angular Gyrus	brain

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