Variant report

Variant	rs55795804
Chromosome Location	chr12:46765946-46765947
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	RCOR1	chr12:46764817-46766002	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr12:46750625-46766899	K562	blood:	n/a	n/a
3	SIX5	chr12:46765523-46767198	A549	lung:	n/a	n/a
4	TAF1	chr12:46764858-46766929	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr12:46764668-46766879	K562	blood:	n/a	n/a
6	POLR2A	chr12:46764536-46766807	GM12878	blood:	n/a	n/a
7	STAT5A	chr12:46764718-46767011	GM12878	blood:	n/a	chr12:46765559-46765570 chr12:46765446-46765458 chr12:46765939-46765947
8	CCNT2	chr12:46764899-46766920	K562	blood:	n/a	chr12:46766229-46766238 chr12:46765520-46765529 chr12:46766029-46766038
9	FOXA1	chr12:46764903-46766896	HepG2	liver:	n/a	chr12:46766358-46766370
10	MYC	chr12:46764918-46767690	NB4	blood:	n/a	chr12:46767168-46767177 chr12:46765212-46765221 chr12:46766078-46766088 chr12:46765212-46765221 chr12:46765212-46765221 chr12:46765210-46765223
11	JUND	chr12:46764013-46766842	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr12:46756521-46767732	H1-hESC	embryonic stem cell:	n/a	n/a
13	YY1	chr12:46765052-46765947	ECC-1	luminal epithelium:	n/a	chr12:46765926-46765935 chr12:46765803-46765814 chr12:46765923-46765934
14	TAF1	chr12:46764776-46766057	A549	lung:	n/a	n/a
15	POLR2A	chr12:46764987-46767683	HCT-116	colon:	n/a	n/a
16	PBX3	chr12:46764946-46766760	A549	lung:	n/a	n/a
17	POLR2A	chr12:46750469-46766708	HepG2	liver:	n/a	n/a
18	NFIC	chr12:46764107-46766064	HepG2	liver:	n/a	n/a
19	REST	chr12:46764583-46767732	H1-neurons	neurons:	n/a	chr12:46766079-46766092 chr12:46766010-46766023 chr12:46765717-46765727 chr12:46765134-46765147 chr12:46767136-46767144
20	POLR2A	chr12:46760573-46767926	Hela-S3	cervix:	n/a	n/a
21	POLR2A	chr12:46750482-46767845	Hela-S3	cervix:	n/a	n/a
22	MAZ	chr12:46764964-46768004	K562	blood:	n/a	chr12:46767168-46767177 chr12:46765212-46765221 chr12:46766078-46766088 chr12:46765212-46765221 chr12:46765212-46765221 chr12:46765210-46765223
23	SP1	chr12:46764683-46767225	A549	lung:	n/a	chr12:46766079-46766088 chr12:46766228-46766242 chr12:46766606-46766618 chr12:46766227-46766239 chr12:46766606-46766617 chr12:46766606-46766618 chr12:46766228-46766237 chr12:46766077-46766089 chr12:46765290-46765301 chr12:46766077-46766089 chr12:46766027-46766039 chr12:46766662-46766673 chr12:46766229-46766238 chr12:46765308-46765319 chr12:46766227-46766239 chr12:46766029-46766038 chr12:46766228-46766238 chr12:46766078-46766087
24	MAX	chr12:46765640-46766811	K562	blood:	n/a	chr12:46766078-46766088
25	POLR2A	chr12:46764638-46766115	SK-N-MC	brain:	n/a	n/a
26	POLR2A	chr12:46754517-46767857	HepG2	liver:	n/a	n/a
27	REST	chr12:46764385-46767290	A549	lung:	n/a	chr12:46766079-46766092 chr12:46766010-46766023 chr12:46765717-46765727 chr12:46765134-46765147 chr12:46767136-46767144
28	SP1	chr12:46764514-46766962	A549	lung:	n/a	chr12:46766079-46766088 chr12:46766228-46766242 chr12:46766606-46766618 chr12:46766227-46766239 chr12:46766606-46766617 chr12:46766606-46766618 chr12:46766228-46766237 chr12:46766077-46766089 chr12:46765290-46765301 chr12:46766077-46766089 chr12:46766027-46766039 chr12:46766662-46766673 chr12:46766229-46766238 chr12:46765308-46765319 chr12:46766227-46766239 chr12:46766029-46766038 chr12:46766228-46766238 chr12:46766078-46766087
29	REST	chr12:46765083-46766865	HL-60	blood:	n/a	chr12:46766079-46766092 chr12:46766010-46766023 chr12:46765717-46765727 chr12:46765134-46765147
30	RAD21	chr12:46764826-46766953	ECC-1	luminal epithelium:	n/a	n/a
31	POLR2A	chr12:46750751-46768006	HepG2	liver:	n/a	n/a
32	GATA3	chr12:46764899-46766725	MCF-7	breast:	n/a	n/a
33	TCF12	chr12:46764708-46767121	SK-N-SH	brain:	n/a	chr12:46765780-46765787 chr12:46765779-46765789 chr12:46765938-46765946 chr12:46765734-46765743
34	MYC	chr12:46765117-46766684	H1-hESC	embryonic stem cell:	n/a	chr12:46765212-46765221 chr12:46766078-46766088 chr12:46765212-46765221 chr12:46765212-46765221 chr12:46765210-46765223
35	POLR2A	chr12:46764821-46767013	H1-neurons	neurons:	n/a	n/a
36	POU2F2	chr12:46764882-46766206	GM12891	blood:	n/a	chr12:46765444-46765456
37	NFIC	chr12:46764785-46766794	ECC-1	luminal epithelium:	n/a	n/a
38	ZBTB7A	chr12:46765012-46767100	ECC-1	luminal epithelium:	n/a	chr12:46765443-46765452 chr12:46766087-46766096
39	TBL1XR1	chr12:46764914-46766940	GM12878	blood:	n/a	n/a
40	FOSL2	chr12:46764937-46765996	MCF-7	breast:	n/a	n/a
41	POLR2A	chr12:46758662-46766869	HUVEC	blood vessel:	n/a	n/a
42	HEY1	chr12:46764536-46766707	HepG2	liver:	n/a	chr12:46766614-46766629 chr12:46766074-46766089 chr12:46765229-46765244
43	MXI1	chr12:46764914-46766897	GM12878	blood:	n/a	chr12:46765211-46765220
44	CHD1	chr12:46764431-46766658	GM12878	blood:	n/a	chr12:46765445-46765455 chr12:46766470-46766477
45	MAX	chr12:46764817-46768138	K562	blood:	n/a	chr12:46767168-46767177 chr12:46765212-46765221 chr12:46766078-46766088 chr12:46765212-46765221 chr12:46765212-46765221 chr12:46765210-46765223
46	POLR2A	chr12:46764754-46765955	GM12892	blood:	n/a	n/a
47	POLR2A	chr12:46764710-46766937	HCT-116	colon:	n/a	n/a
48	CHD1	chr12:46763609-46766632	H1-hESC	embryonic stem cell:	n/a	chr12:46765445-46765455 chr12:46766470-46766477
49	SMC3	chr12:46764814-46766497	K562	blood:	n/a	chr12:46765660-46765670
50	CHD1	chr12:46756240-46768821	IMR90	lung:	n/a	chr12:46765445-46765455 chr12:46766470-46766477 chr12:46768496-46768506 chr12:46768499-46768509

No.	Distal block	Cell Line	Cell type
1	chr12:46656458..46664971-chr12:46763618..46767965,19	MCF-7	breast:
2	chr12:46765236..46766145-chr14:91976344..91977306,2	Hela-S3	cervix:
3	chr10:43931979..43932697-chr12:46765935..46766466,2	Hela-S3	cervix:
4	chr12:46652597..46666608-chr12:46757245..46767985,36	MCF-7	breast:
5	chr12:46765902..46766852-chr4:99849792..99850426,2	Hela-S3	cervix:
6	chr1:70819966..70820788-chr12:46765760..46766512,2	Hela-S3	cervix:
7	chr12:46381030..46386260-chr12:46762457..46768592,6	K562	blood:
8	chr12:46383804..46386112-chr12:46763445..46766511,3	MCF-7	breast:
9	chr12:46765839..46766539-chr12:46777338..46778283,2	Hela-S3	cervix:
10	chr12:46765942..46766621-chr4:48782002..48782569,2	Hela-S3	cervix:
11	chr12:46765461..46766204-chr17:41466077..41466603,2	Hela-S3	cervix:
12	chr12:46765603..46767339-chr12:49452531..49455344,2	K562	blood:
13	chr12:46119720..46123062-chr12:46761797..46766025,4	K562	blood:
14	chr12:46119720..46122632-chr12:46763272..46766407,3	K562	blood:
15	chr12:46381426..46387093-chr12:46763754..46767064,8	MCF-7	breast:
16	chr12:46765633..46766475-chr8:56986662..56987222,2	Hela-S3	cervix:
17	chr12:46765278..46766276-chr17:28804033..28804821,2	Hela-S3	cervix:
18	chr12:46659532..46664131-chr12:46762494..46766775,7	K562	blood:
19	chr12:46765232..46766177-chr19:15490140..15490969,2	Hela-S3	cervix:
20	chr12:46765626..46766493-chr2:10262224..10262953,2	Hela-S3	cervix:
21	chr12:46765776..46766454-chr6:26056231..26056873,3	Hela-S3	cervix:
22	chr12:46658047..46664131-chr12:46762494..46767686,10	K562	blood:
23	chr11:62494567..62495103-chr12:46765368..46766321,2	Hela-S3	cervix:
24	chr12:46382586..46387481-chr12:46763277..46769922,9	K562	blood:
25	chr12:46765748..46766647-chr12:93835599..93836248,2	Hela-S3	cervix:
26	chr12:46765505..46766040-chr16:376938..377806,2	Hela-S3	cervix:
27	chr12:46765728..46766610-chr16:89626631..89627379,2	HCT-116	colon:
28	chr11:65266501..65267444-chr12:46765211..46766513,3	Hela-S3	cervix:
29	chr12:46765792..46766591-chrX:40594883..40595718,2	Hela-S3	cervix:
30	chr12:46765886..46766791-chr16:2517745..2518650,2	Hela-S3	cervix:
31	chr12:46765279..46767485-chr19:45580991..45583480,2	MCF-7	breast:

Variant related genes	Relation type
SLC38A2	TF binding region
ENSG00000177889	Chromatin interaction
ENSG00000171848	Chromatin interaction
ENSG00000234857	Chromatin interaction
ENSG00000180182	Chromatin interaction
ENSG00000151247	Chromatin interaction
ENSG00000007047	Chromatin interaction
ENSG00000273015	Chromatin interaction
ENSG00000263923	Chromatin interaction
ENSG00000259895	Chromatin interaction
ENSG00000118454	Chromatin interaction
ENSG00000253603	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000142252	Chromatin interaction
ENSG00000008988	Chromatin interaction
ENSG00000100796	Chromatin interaction
ENSG00000197568	Chromatin interaction
ENSG00000105127	Chromatin interaction
ENSG00000139218	Chromatin interaction
ENSG00000075539	Chromatin interaction
ENSG00000108587	Chromatin interaction
ENSG00000187837	Chromatin interaction
ENSG00000188825	Chromatin interaction
ENSG00000214753	Chromatin interaction
ENSG00000257261	Chromatin interaction
ENSG00000167548	Chromatin interaction
ENSG00000167526	Chromatin interaction
ENSG00000243660	Chromatin interaction
ENSG00000111371	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11183453	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11833812	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11834593	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17096884	0.81[ASN][1000 genomes]
rs1948425	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2307059	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3742061	0.81[ASN][1000 genomes]
rs57199226	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57425661	0.81[ASN][1000 genomes]
rs57786829	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58545634	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59546893	0.87[EUR][1000 genomes]
rs61406609	0.81[ASN][1000 genomes]
rs73282593	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7967840	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832398	chr12:46611692-46825530	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers 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	181 gene(s)	inside rSNPs	diseases
2	esv1842882	chr12:46691487-47009428	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
3	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	esv3429861	chr12:46762813-46988789	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	145 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	chr12:46755400-46766000	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr12:46756800-46766000	Transcr. at gene 5' and 3'	NHLF	lung
3	chr12:46757400-46766000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
4	chr12:46758800-46766000	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr12:46758800-46766000	Transcr. at gene 5' and 3'	NHEK	skin
6	chr12:46760400-46766200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr12:46760600-46766000	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr12:46760600-46766000	Transcr. at gene 5' and 3'	Dnd41	blood
9	chr12:46761200-46766400	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum
10	chr12:46761600-46766000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
11	chr12:46762200-46767800	Active TSS	Right Ventricle	heart
12	chr12:46762400-46767000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
13	chr12:46763400-46767400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr12:46763400-46767800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr12:46763600-46767600	Active TSS	Ovary	ovary
16	chr12:46763600-46767600	Active TSS	Psoas Muscle	Psoas
17	chr12:46763800-46767200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr12:46763800-46767200	Active TSS	Fetal Intestine Small	intestine
19	chr12:46764400-46767000	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr12:46764400-46767000	Active TSS	Fetal Intestine Large	intestine
21	chr12:46764400-46767200	Active TSS	Rectal Mucosa Donor 31	rectum
22	chr12:46764400-46767600	Active TSS	Fetal Muscle Trunk	muscle
23	chr12:46764400-46767600	Active TSS	Small Intestine	intestine
24	chr12:46764400-46767600	Active TSS	HSMMtube	muscle
25	chr12:46764400-46767800	Bivalent/Poised TSS	HepG2	liver
26	chr12:46764400-46768000	Active TSS	Lung	lung
27	chr12:46764400-46768000	Active TSS	Rectal Smooth Muscle	rectum
28	chr12:46764600-46767400	Active TSS	Primary monocytes fromperipheralblood	blood
29	chr12:46764600-46767400	Active TSS	Duodenum Mucosa	Duodenum
30	chr12:46764600-46767400	Active TSS	Monocytes-CD14+_RO01746	blood
31	chr12:46764600-46767800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr12:46764600-46767800	Active TSS	Brain Anterior Caudate	brain
33	chr12:46764600-46767800	Active TSS	Colon Smooth Muscle	Colon
34	chr12:46764800-46767000	Active TSS	Brain Hippocampus Middle	brain
35	chr12:46764800-46767200	Active TSS	Fetal Brain Female	brain
36	chr12:46764800-46767400	Active TSS	Primary T cells from cord blood	blood
37	chr12:46764800-46767400	Active TSS	Pancreas	Pancrea
38	chr12:46764800-46767400	Active TSS	Spleen	Spleen
39	chr12:46764800-46767600	Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr12:46764800-46767600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr12:46764800-46767600	Active TSS	Brain Substantia Nigra	brain
42	chr12:46764800-46767600	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr12:46764800-46767600	Active TSS	Gastric	stomach
44	chr12:46765000-46766400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr12:46765000-46766400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr12:46765000-46766600	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr12:46765000-46766600	Active TSS	Primary B cells from cord blood	blood
48	chr12:46765000-46766800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
49	chr12:46765000-46766800	Active TSS	Primary T helper cells fromperipheralblood	blood
50	chr12:46765000-46766800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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