Variant report

Variant	rs4852953
Chromosome Location	chr2:73869908-73869909
allele	A/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	RCOR1	chr2:73869814-73870102	HepG2	liver:	n/a	n/a
2	JUND	chr2:73869869-73870172	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:73869519-73870096	HepG2	liver:	n/a	n/a
4	HNF4A	chr2:73869856-73870115	HepG2	liver:	n/a	chr2:73870067-73870083
5	FOXA1	chr2:73869459-73870306	HepG2	liver:	n/a	n/a
6	FOSL2	chr2:73869269-73870339	HepG2	liver:	n/a	n/a
7	FOXA2	chr2:73869546-73870382	HepG2	liver:	n/a	n/a
8	SP1	chr2:73869313-73870328	HepG2	liver:	n/a	n/a
9	ELF1	chr2:73869861-73870204	HepG2	liver:	n/a	n/a
10	ELF1	chr2:73869815-73870194	HepG2	liver:	n/a	n/a
11	HNF4A	chr2:73869834-73870162	HepG2	liver:	n/a	chr2:73870067-73870083
12	MAX	chr2:73869553-73870202	HepG2	liver:	n/a	n/a
13	TBP	chr2:73869792-73870084	HepG2	liver:	n/a	n/a
14	MYBL2	chr2:73869303-73870321	HepG2	liver:	n/a	n/a
15	JUND	chr2:73869895-73870147	HepG2	liver:	n/a	n/a
16	MXI1	chr2:73869517-73870246	HepG2	liver:	n/a	n/a
17	FOXA2	chr2:73869822-73870269	HepG2	liver:	n/a	n/a
18	YY1	chr2:73869738-73870221	HepG2	liver:	n/a	n/a
19	MAX	chr2:73869818-73870190	HepG2	liver:	n/a	n/a
20	FOXA1	chr2:73869381-73870259	HepG2	liver:	n/a	n/a
21	EP300	chr2:73869817-73870139	HepG2	liver:	n/a	chr2:73870048-73870055
22	POLR2A	chr2:73869299-73870205	HepG2	liver:	n/a	n/a
23	MBD4	chr2:73869415-73870213	HepG2	liver:	n/a	n/a
24	EP300	chr2:73869820-73870261	HepG2	liver:	n/a	chr2:73870048-73870055
25	RXRA	chr2:73869361-73870351	HepG2	liver:	n/a	chr2:73869666-73869686
26	MBD4	chr2:73869461-73870194	HepG2	liver:	n/a	n/a
27	HEY1	chr2:73869257-73870291	HepG2	liver:	n/a	n/a
28	FOXA1	chr2:73869511-73870290	HepG2	liver:	n/a	n/a
29	NFIC	chr2:73869458-73870216	HepG2	liver:	n/a	chr2:73869883-73869900
30	FOSL2	chr2:73869758-73870241	HepG2	liver:	n/a	n/a
31	CHD2	chr2:73869804-73870074	HepG2	liver:	n/a	n/a
32	HDAC2	chr2:73869852-73870210	HepG2	liver:	n/a	n/a
33	MYBL2	chr2:73868990-73870320	HepG2	liver:	n/a	n/a
34	FOXA1	chr2:73869463-73870323	HepG2	liver:	n/a	n/a
35	TEAD4	chr2:73869262-73870386	HepG2	liver:	n/a	n/a
36	RXRA	chr2:73869292-73870550	HepG2	liver:	n/a	chr2:73870398-73870405 chr2:73869666-73869686
37	SIN3AK20	chr2:73869866-73870175	HepG2	liver:	n/a	n/a
38	JUND	chr2:73869853-73870254	HepG2	liver:	n/a	n/a
39	MAFF	chr2:73869629-73870072	HepG2	liver:	n/a	n/a
40	ARID3A	chr2:73869857-73870120	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:73868945..73872912-chr2:73927731..73932752,4	MCF-7	breast:

Variant related genes	Relation type
NAT8	TF binding region
ALMS1P	TF binding region
ENSG00000204872	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11126407	0.84[ASN][1000 genomes]
rs11126408	0.84[ASN][1000 genomes]
rs11126409	0.84[ASN][1000 genomes]
rs11126411	0.82[ASN][1000 genomes]
rs12151671	0.84[ASN][1000 genomes]
rs12478871	0.82[ASN][1000 genomes]
rs12620569	0.84[ASN][1000 genomes]
rs12991161	0.86[ASN][1000 genomes]
rs13007607	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13007623	0.84[ASN][1000 genomes]
rs13018422	0.84[AMR][1000 genomes]
rs13022145	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13027816	0.84[ASN][1000 genomes]
rs1879662	0.83[ASN][1000 genomes]
rs1879666	0.84[ASN][1000 genomes]
rs2280506	0.83[ASN][1000 genomes]
rs2280507	0.83[ASN][1000 genomes]
rs2421584	0.84[ASN][1000 genomes]
rs2421586	0.83[ASN][1000 genomes]
rs2421587	0.81[ASN][1000 genomes]
rs2421589	0.82[ASN][1000 genomes]
rs2421590	0.84[ASN][1000 genomes]
rs2421591	0.82[ASN][1000 genomes]
rs28708576	0.83[ASN][1000 genomes]
rs34719281	0.84[ASN][1000 genomes]
rs34874205	0.85[ASN][1000 genomes]
rs4341964	0.83[ASN][1000 genomes]
rs4443018	0.83[ASN][1000 genomes]
rs4627598	0.81[ASN][1000 genomes]
rs4852310	0.84[ASN][1000 genomes]
rs4852948	0.83[ASN][1000 genomes]
rs4852949	0.84[ASN][1000 genomes]
rs4852950	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4852951	0.86[ASN][1000 genomes]
rs4852954	0.84[ASN][1000 genomes]
rs4852956	0.82[ASN][1000 genomes]
rs4852957	0.88[ASN][1000 genomes]
rs4852958	0.81[ASN][1000 genomes]
rs4852959	0.83[AMR][1000 genomes]
rs6546862	0.86[ASN][1000 genomes]
rs6546863	0.84[ASN][1000 genomes]
rs6718799	0.82[ASN][1000 genomes]
rs6725284	0.81[ASN][1000 genomes]
rs6729347	0.84[ASN][1000 genomes]
rs6744273	0.83[ASN][1000 genomes]
rs6755948	0.85[ASN][1000 genomes]
rs7570683	0.84[ASN][1000 genomes]
rs7574268	0.83[ASN][1000 genomes]
rs7579068	0.81[ASN][1000 genomes]
rs7585668	0.84[ASN][1000 genomes]
rs7607989	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:32 , 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	nsv874268	chr2:73837751-73907696	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv874269	chr2:73837751-73914019	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv874270	chr2:73837751-73916672	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1015036	chr2:73840055-73891004	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1006235	chr2:73840055-73896603	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1006033	chr2:73840055-73900856	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	esv2760600	chr2:73846605-73911523	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv874271	chr2:73847024-73907696	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv874272	chr2:73847024-73914019	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv874273	chr2:73847024-73916672	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv874274	chr2:73847024-73922475	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	nsv874275	chr2:73847024-73931971	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv874276	chr2:73847024-73964214	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
18	nsv979021	chr2:73847283-73871861	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
19	nsv1013586	chr2:73848777-73906844	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	nsv1004208	chr2:73849172-73911511	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
21	esv2497164	chr2:73850717-73912022	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
22	nsv1004886	chr2:73852525-73900856	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
23	nsv1011488	chr2:73852525-73909818	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
24	nsv1000057	chr2:73852525-73911511	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
25	esv3385057	chr2:73853505-73913858	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
26	nsv1013142	chr2:73854911-73911511	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
27	nsv1008311	chr2:73854911-73923089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
28	nsv829460	chr2:73856145-73913711	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
29	nsv582209	chr2:73857002-73907696	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
30	nsv818044	chr2:73859184-73906819	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
31	nsv515605	chr2:73859184-73916672	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
32	esv3334222	chr2:73867401-73923991	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4852953	TPRKB	Cis_1M	lymphoblastoid	RTeQTL
rs4852953	ALMS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73866200-73870600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr2:73866400-73871200	Enhancers	Fetal Lung	lung
3	chr2:73867000-73872200	Enhancers	Ovary	ovary
4	chr2:73867400-73870200	Flanking Active TSS	Liver	Liver
5	chr2:73867400-73870200	Enhancers	Fetal Intestine Large	intestine
6	chr2:73867600-73872200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr2:73867800-73870000	Enhancers	Placenta	Placenta
8	chr2:73868200-73870000	Enhancers	Fetal Intestine Small	intestine
9	chr2:73868400-73871000	Weak transcription	Spleen	Spleen
10	chr2:73868400-73871400	Enhancers	Primary hematopoietic stem cells	blood
11	chr2:73868600-73877000	Weak transcription	Gastric	stomach
12	chr2:73869000-73870200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:73869000-73870200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
14	chr2:73869000-73870400	Flanking Active TSS	HepG2	liver
15	chr2:73869400-73870200	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr2:73869600-73870000	Enhancers	Stomach Mucosa	stomach
17	chr2:73869600-73870000	Bivalent Enhancer	HUVEC	blood vessel
18	chr2:73869600-73870200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:73869600-73870200	Enhancers	Fetal Kidney	kidney
20	chr2:73869600-73872000	Enhancers	Lung	lung
21	chr2:73869800-73870000	Enhancers	Duodenum Mucosa	Duodenum
22	chr2:73869800-73870000	Enhancers	Left Ventricle	heart
23	chr2:73869800-73870000	Enhancers	Rectal Mucosa Donor 29	rectum
24	chr2:73869800-73870200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr2:73869800-73870200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr2:73869800-73870200	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr2:73869800-73870200	Enhancers	A549	lung
28	chr2:73869800-73870400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr2:73869800-73870400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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