Variant report

Variant	rs13006598
Chromosome Location	chr2:74010592-74010593
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOSL2	chr2:74010378-74010865	A549	lung:	n/a	chr2:74010778-74010789
2	HEY1	chr2:74010441-74010908	HepG2	liver:	n/a	n/a
3	USF1	chr2:74010528-74010763	H1-hESC	embryonic stem cell:	n/a	chr2:74010683-74010694
4	USF1	chr2:74010544-74010750	HepG2	liver:	n/a	chr2:74010683-74010694
5	POLR2A	chr2:74010460-74010764	HCT-116	colon:	n/a	n/a
6	JUND	chr2:74010575-74010877	HepG2	liver:	n/a	chr2:74010779-74010790
7	FOSL2	chr2:74010457-74011032	HepG2	liver:	n/a	chr2:74010778-74010789
8	USF1	chr2:74010542-74010781	HepG2	liver:	n/a	chr2:74010683-74010694
9	FOSL2	chr2:74010094-74010934	HepG2	liver:	n/a	chr2:74010778-74010789
10	MAX	chr2:74010528-74010863	A549	lung:	n/a	n/a
11	POLR2A	chr2:74010516-74010855	HCT-116	colon:	n/a	n/a
12	JUND	chr2:74010496-74010969	HepG2	liver:	n/a	chr2:74010779-74010790
13	MAX	chr2:74010379-74010877	A549	lung:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:74010554-74010604	AG04450	lung:	fetal
2	chr2:74010554-74010604	AG09309	skin:	n/a
3	chr2:74010554-74010604	AG09319	gingival:	n/a
4	chr2:74010554-74010604	CMK	blood:	n/a
5	chr2:74010554-74010604	NT2-D1	testis:	n/a
6	chr2:74010554-74010604	GM12891	blood:	n/a
7	chr2:74010554-74010604	SK-N-SH	brain:	n/a
8	chr2:74010554-74010604	GM12878	blood:	n/a
9	chr2:74010554-74010604	NHBE	bronchial:	n/a
10	chr2:74010554-74010604	HepG2	liver:	n/a
11	chr2:74010554-74010604	SK-N-SH_RA	brain:	n/a
12	chr2:74010554-74010604	HCM	heart:	n/a
13	chr2:74010554-74010604	GM06990	blood:	n/a
14	chr2:74010554-74010604	H1-hESC	embryonic stem cell:	embryo
15	chr2:74010554-74010604	HL-60	blood:	n/a
16	chr2:74010554-74010604	AG10803	skin:	n/a
17	chr2:74010554-74010604	HMEC	breast:	n/a
18	chr2:74010554-74010604	HRCEpiC	kidney:	n/a
19	chr2:74010554-74010604	HIPEpiC	eye:	n/a
20	chr2:74010554-74010604	AoSMC	blood vessel:	n/a
21	chr2:74010554-74010604	HUVEC	blood vessel:	n/a
22	chr2:74010554-74010604	BJ	skin:	n/a
23	chr2:74010554-74010604	NH-A	brain:	n/a
24	chr2:74010554-74010604	K562	blood:	n/a
25	chr2:74010554-74010604	AG04449	skin:	fetal
26	chr2:74010554-74010604	SKMC	muscle:	n/a
27	chr2:74010554-74010604	Caco-2	colon:	n/a
28	chr2:74010554-74010604	U87	brain:	n/a
29	chr2:74010554-74010604	BE2_C	brain:	n/a
30	chr2:74010554-74010604	RPTEC	kidney:	n/a
31	chr2:74010554-74010604	HRE	kidney:	n/a
32	chr2:74010554-74010604	NB4	blood:	n/a
33	chr2:74010554-74010604	HCPEpiC	choroid plexus:	n/a
34	chr2:74010554-74010604	MCF-7	breast:	n/a
35	chr2:74010554-74010604	HNPCEpiC	eye:	n/a
36	chr2:74010554-74010604	Hepatocyte	liver:	n/a
37	chr2:74010554-74010604	HAEpiC	amniotic membrane:	n/a
38	chr2:74010554-74010604	SK-N-MC	brain:	n/a
39	chr2:74010554-74010604	GM19239	blood:	n/a
40	chr2:74010554-74010604	IMR90	lung:	fetal
41	chr2:74010554-74010604	PANC-1	pancreas:	n/a
42	chr2:74010554-74010604	SAEC	small airway:	n/a
43	chr2:74010554-74010604	ECC-1	luminal epithelium:	n/a
44	chr2:74010554-74010604	T-47D	breast:	n/a
45	chr2:74010554-74010604	Hela-S3	cervix:	n/a
46	chr2:74010554-74010604	ProgFib	skin:	n/a
47	chr2:74010554-74010604	HRPEpiC	eye:	n/a
48	chr2:74010554-74010604	Jurkat	blood:	n/a
49	chr2:74010554-74010604	A549	lung:	n/a
50	chr2:74010554-74010604	LNCaP	prostate:	n/a

No data

Variant related genes	Relation type
DUSP11	TF binding region
C2orf78	TF binding region
C2orf78	CpG island
DUSP11	CpG island

Extended variants
information (count: 114 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10172044	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10191988	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10193032	0.98[ASN][1000 genomes]
rs10203740	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10208995	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11126415	0.87[EUR][1000 genomes]
rs11126416	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11126417	0.93[EUR][1000 genomes]
rs11891140	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11892172	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11894953	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12052539	0.87[EUR][1000 genomes]
rs12053242	0.87[EUR][1000 genomes]
rs12233112	0.87[AMR][1000 genomes]
rs12615807	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12619258	0.85[AMR][1000 genomes]
rs12624267	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12713789	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12713790	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12713791	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12713793	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12713794	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12713795	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12713797	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12713798	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12992607	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12997568	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13003035	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13005729	0.84[AMR][1000 genomes]
rs13006448	0.84[AMR][1000 genomes]
rs13013228	0.84[AMR][1000 genomes]
rs13014700	0.83[AMR][1000 genomes]
rs13015885	0.83[AMR][1000 genomes]
rs13020517	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13031853	0.84[AMR][1000 genomes]
rs13031866	0.85[AMR][1000 genomes]
rs13033744	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13383097	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17350056	0.86[AMR][1000 genomes]
rs17350125	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17350188	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17434655	0.81[AMR][1000 genomes]
rs1806683	0.87[EUR][1000 genomes]
rs1815028	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2001436	0.81[AMR][1000 genomes]
rs2001490	0.81[AMR][1000 genomes]
rs2006997	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2012574	0.85[AMR][1000 genomes]
rs2116367	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2272051	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2272178	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2421557	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2421558	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2421559	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2421575	0.83[AMR][1000 genomes]
rs2421672	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2421674	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2421675	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2421676	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2421677	0.89[EUR][1000 genomes]
rs2462127	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35498419	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35767294	0.84[AMR][1000 genomes]
rs35791379	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3813228	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3980695	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4241257	0.87[EUR][1000 genomes]
rs4358149	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4513320	0.82[AMR][1000 genomes]
rs4852316	0.85[EUR][1000 genomes]
rs4852975	0.87[AMR][1000 genomes]
rs4852976	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4852977	0.87[EUR][1000 genomes]
rs4852978	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6748233	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6749841	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6750494	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6750515	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6750877	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6755500	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7210	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs732778	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7368570	0.81[AMR][1000 genomes]
rs7558546	0.87[EUR][1000 genomes]
rs7591112	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7597302	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7599453	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs891695	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs891696	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9309475	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9309476	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428051	chr2:73717032-74030067	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2757806	chr2:73717032-74078592	Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv2759060	chr2:73717032-74078592	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1013385	chr2:73822056-74041441	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv834260	chr2:73906106-74076520	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv1000675	chr2:73919185-74038946	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv2780	chr2:73994168-74057248	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	esv1828210	chr2:74005068-74038451	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	esv1798760	chr2:74008555-74037432	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	esv1796755	chr2:74008755-74037232	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	esv1829180	chr2:74008755-74040242	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv10024	chr2:74009680-74037260	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
13	esv12664	chr2:74009707-74039385	Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv471530	chr2:74009713-74037182	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv963622	chr2:74009937-74011888	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
16	esv3371250	chr2:74010144-74014742	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island	2 gene(s)	inside rSNPs	diseases
17	esv1794852	chr2:74010258-74036308	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
18	esv1831787	chr2:74010258-74036308	Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
19	esv1795724	chr2:74010341-74036605	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
20	esv1830089	chr2:74010341-74036605	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
21	esv1830247	chr2:74010341-74036605	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
22	esv1803581	chr2:74010541-74038731	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
23	esv1825297	chr2:74010541-74040242	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13006598	ALMS1	Cis_1M	lymphoblastoid	RTeQTL
rs13006598	TPRKB	Cis_1M	lymphoblastoid	RTeQTL
rs13006598	ALMS1P	cis	Nerve Tibial	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74010000-74010600	Enhancers	NHEK	skin
2	chr2:74010000-74010800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:74010000-74010800	Enhancers	Hela-S3	cervix
4	chr2:74010000-74011000	Enhancers	HMEC	breast
5	chr2:74010200-74010600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr2:74010200-74010800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr2:74010400-74010600	Flanking Active TSS	A549	lung
8	chr2:74010400-74010600	Bivalent/Poised TSS	HepG2	liver
9	chr2:74010400-74010800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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