Variant report

Variant	rs573544156
Chromosome Location	chr12:49760122-49760123
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	SIX5	chr12:49760108-49761102	A549	lung:	n/a	n/a
2	NFIC	chr12:49760014-49761408	GM12878	blood:	n/a	n/a
3	GATA3	chr12:49760022-49761395	MCF-7	breast:	n/a	chr12:49761286-49761296
4	POLR2A	chr12:49759832-49761928	HepG2	liver:	n/a	n/a
5	SIN3AK20	chr12:49760100-49761469	HCT-116	colon:	n/a	n/a
6	TCF12	chr12:49759904-49761442	A549	lung:	n/a	n/a
7	ZBTB7A	chr12:49759978-49761950	ECC-1	luminal epithelium:	n/a	chr12:49760348-49760357 chr12:49760266-49760277
8	POLR2A	chr12:49760092-49761646	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr12:49759876-49761869	HUVEC	blood vessel:	n/a	n/a
10	E2F6	chr12:49760071-49761083	H1-hESC	embryonic stem cell:	n/a	chr12:49760347-49760356 chr12:49761071-49761080 chr12:49761008-49761018 chr12:49761026-49761035 chr12:49760342-49760354 chr12:49760596-49760606
11	SIN3A	chr12:49760085-49761782	H1-hESC	embryonic stem cell:	n/a	chr12:49760195-49760209 chr12:49760196-49760205
12	MAX	chr12:49760046-49761398	ECC-1	luminal epithelium:	n/a	n/a
13	RUNX3	chr12:49759998-49762249	GM12878	blood:	n/a	n/a
14	POLR2A	chr12:49759988-49761715	ECC-1	luminal epithelium:	n/a	n/a
15	NR2F2	chr12:49759935-49761333	K562	blood:	n/a	n/a
16	POLR2A	chr12:49759981-49761955	GM12878	blood:	n/a	n/a
17	SP1	chr12:49760041-49761714	A549	lung:	n/a	chr12:49761093-49761102 chr12:49761094-49761103 chr12:49761094-49761103 chr12:49761092-49761104 chr12:49760770-49760784 chr12:49761195-49761206 chr12:49761092-49761104
18	ZBTB7A	chr12:49760046-49760395	HepG2	liver:	n/a	chr12:49760348-49760357 chr12:49760266-49760277
19	CREB1	chr12:49760090-49761440	H1-hESC	embryonic stem cell:	n/a	n/a
20	POU2F2	chr12:49759900-49760347	GM12891	blood:	n/a	n/a
21	POLR2A	chr12:49759971-49761777	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr12:49760078-49761401	GM12891	blood:	n/a	n/a
23	SIN3AK20	chr12:49760096-49760946	A549	lung:	n/a	n/a
24	STAT5A	chr12:49759985-49761885	GM12878	blood:	n/a	chr12:49760790-49760802
25	REST	chr12:49760096-49762199	H1-neurons	neurons:	n/a	chr12:49761766-49761779 chr12:49761322-49761335 chr12:49760355-49760368 chr12:49761766-49761779 chr12:49760196-49760206 chr12:49760194-49760208
26	MAX	chr12:49760074-49761450	HepG2	liver:	n/a	n/a
27	PML	chr12:49760071-49761424	GM12878	blood:	n/a	n/a
28	YY1	chr12:49760121-49761410	HepG2	liver:	n/a	n/a
29	TAF1	chr12:49760010-49761454	ECC-1	luminal epithelium:	n/a	n/a
30	POLR2A	chr12:49759989-49761434	K562	blood:	n/a	n/a
31	MTA3	chr12:49760075-49761383	GM12878	blood:	n/a	n/a
32	POLR2A	chr12:49759944-49761905	GM12878	blood:	n/a	n/a
33	MYBL2	chr12:49760093-49761363	HepG2	liver:	n/a	n/a
34	SMARCC1	chr12:49760092-49761300	Hela-S3	cervix:	n/a	n/a
35	NFATC1	chr12:49760041-49761047	GM12878	blood:	n/a	n/a
36	RUNX3	chr12:49760024-49761432	GM12878	blood:	n/a	n/a
37	MAX	chr12:49759984-49761429	K562	blood:	n/a	n/a
38	MAX	chr12:49760122-49761440	SK-N-SH	brain:	n/a	n/a
39	ELF1	chr12:49760119-49760879	MCF-7	breast:	n/a	chr12:49760356-49760368
40	ELF1	chr12:49760061-49761677	GM12878	blood:	n/a	chr12:49760356-49760368 chr12:49761322-49761334
41	MAX	chr12:49759996-49761458	A549	lung:	n/a	n/a
42	POLR2A	chr12:49759885-49761730	PFSK-1	brain:	n/a	n/a
43	POLR2A	chr12:49759976-49761452	PANC-1	pancreas:	n/a	n/a
44	E2F6	chr12:49760112-49761440	A549	lung:	n/a	chr12:49760347-49760356 chr12:49761071-49761080 chr12:49761008-49761018 chr12:49761026-49761035 chr12:49760342-49760354 chr12:49760596-49760606
45	POLR2A	chr12:49760122-49760179	GM12878	blood:	n/a	n/a
46	NRF1	chr12:49760038-49761957	SK-N-SH	brain:	n/a	chr12:49760978-49760989 chr12:49760597-49760606 chr12:49761070-49761079 chr12:49761024-49761035 chr12:49761067-49761081 chr12:49760347-49760356 chr12:49761070-49761081
47	ZBTB7A	chr12:49760026-49761981	ECC-1	luminal epithelium:	n/a	chr12:49760348-49760357 chr12:49760266-49760277
48	SIN3AK20	chr12:49760103-49761449	SK-N-SH	brain:	n/a	n/a
49	POLR2A	chr12:49760088-49761456	GM12878	blood:	n/a	n/a
50	TAF1	chr12:49759983-49761776	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:49716623..49719210-chr12:49759055..49761901,3	MCF-7	breast:
2	chr12:49656837..49661590-chr12:49759665..49765017,7	K562	blood:
3	chr12:49657571..49662873-chr12:49757027..49762131,10	K562	blood:
4	chr12:49740569..49744952-chr12:49759719..49761508,3	K562	blood:
5	chr12:49390072..49392510-chr12:49759241..49762093,2	K562	blood:
6	chr12:49759499..49761453-chr12:49953026..49955590,2	MCF-7	breast:
7	chr12:49759487..49762377-chr12:49960316..49963479,6	K562	blood:
8	chr12:49759658..49762377-chr12:49960316..49963047,2	K562	blood:
9	chr12:49758876..49762155-chr12:49906533..49909731,5	MCF-7	breast:
10	chr12:49717382..49719680-chr12:49758980..49761177,3	K562	blood:
11	chr12:49758243..49761237-chr12:50135535..50137212,2	MCF-7	breast:
12	chr12:49757911..49761864-chr12:50015854..50019350,3	K562	blood:
13	chr12:49759630..49760473-chr12:49907526..49908336,2	MCF-7	breast:
14	chr12:49759096..49761213-chr12:49881834..49884299,3	K562	blood:
15	chr12:49759519..49761735-chr12:49853453..49856491,3	K562	blood:
16	chr12:49758102..49760925-chr12:49950793..49953218,2	MCF-7	breast:
17	chr12:49759638..49761406-chr12:49937675..49939250,2	MCF-7	breast:
18	chr12:49759045..49761163-chr12:50015602..50018404,2	MCF-7	breast:
19	chr12:49759192..49762198-chr12:50016828..50018696,3	MCF-7	breast:
20	chr12:49745336..49748188-chr12:49759488..49762139,2	K562	blood:
21	chr12:49759029..49763168-chr12:49779946..49784312,5	MCF-7	breast:
22	chr12:49729980..49733163-chr12:49759007..49762779,4	K562	blood:
23	chr12:49760076..49762481-chr12:49958970..49962083,4	MCF-7	breast:
24	chr12:49757995..49761023-chr12:49883452..49885795,3	MCF-7	breast:
25	chr12:49740075..49745225-chr12:49756992..49761732,8	K562	blood:
26	chr12:49759421..49761447-chr17:56735493..56738018,2	MCF-7	breast:
27	chr12:49759353..49761548-chr12:49931777..49934189,4	K562	blood:
28	chr12:49759353..49762276-chr12:49930939..49933731,4	K562	blood:
29	chr12:49759570..49762166-chr12:49852805..49855688,2	MCF-7	breast:
30	chr12:49739131..49745064-chr12:49758784..49762517,10	MCF-7	breast:
31	chr12:49740264..49744957-chr12:49759411..49762039,7	MCF-7	breast:
32	chr12:49730111..49734791-chr12:49758969..49762593,4	MCF-7	breast:

Variant related genes	Relation type
SPATS2	TF binding region
ENSG00000135519	Chromatin interaction
ENSG00000257913	Chromatin interaction
ENSG00000186897	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000135451	Chromatin interaction
ENSG00000139644	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000110844	Chromatin interaction
ENSG00000178401	Chromatin interaction
ENSG00000258334	Chromatin interaction
ENSG00000123352	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000187778	Chromatin interaction
ENSG00000257954	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv1042122	chr12:49678529-49823168	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
5	nsv1039176	chr12:49678529-49832618	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
6	nsv899068	chr12:49714103-49924637	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv832405	chr12:49720279-49910862	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
8	esv3423651	chr12:49760110-49762658	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49758800-49760200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr12:49759200-49760400	Flanking Active TSS	NHEK	skin
3	chr12:49759400-49760200	Flanking Active TSS	Dnd41	blood
4	chr12:49759600-49760200	Enhancers	Spleen	Spleen
5	chr12:49759600-49760200	Active TSS	HepG2	liver
6	chr12:49759600-49760400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr12:49759600-49760400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:49759600-49760400	Flanking Active TSS	K562	blood
9	chr12:49759600-49760600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr12:49759600-49762000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:49759600-49762000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:49759600-49762200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr12:49759600-49762600	Active TSS	H1 Cell Line	embryonic stem cell
14	chr12:49759600-49762600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr12:49759600-49763000	Active TSS	A549	lung
16	chr12:49759800-49760200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr12:49759800-49760400	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr12:49759800-49760400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
19	chr12:49759800-49760400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr12:49759800-49760400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr12:49759800-49760400	Flanking Active TSS	Stomach Smooth Muscle	stomach
22	chr12:49759800-49760400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr12:49759800-49761000	Enhancers	Fetal Brain Male	brain
24	chr12:49759800-49761600	Active TSS	Placenta	Placenta
25	chr12:49759800-49761600	Active TSS	Rectal Mucosa Donor 31	rectum
26	chr12:49759800-49761600	Active TSS	Rectal Smooth Muscle	rectum
27	chr12:49759800-49761800	Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr12:49759800-49761800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr12:49759800-49761800	Active TSS	Cortex derived primary cultured neurospheres	brain
30	chr12:49759800-49761800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr12:49759800-49761800	Active TSS	Hela-S3	cervix
32	chr12:49759800-49762000	Active TSS	ES-I3 Cell Line	embryonic stem cell
33	chr12:49759800-49762000	Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr12:49759800-49762000	Active TSS	HUES64 Cell Line	embryonic stem cell
35	chr12:49759800-49762000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:49759800-49762200	Active TSS	H9 Cell Line	embryonic stem cell
37	chr12:49759800-49762200	Active TSS	Colonic Mucosa	Colon
38	chr12:49759800-49762200	Active TSS	Fetal Intestine Large	intestine
39	chr12:49759800-49762400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr12:49759800-49762600	Active TSS	HSMM	muscle
41	chr12:49759800-49763200	Active TSS	GM12878-XiMat	blood
42	chr12:49759800-49764000	Active TSS	Rectal Mucosa Donor 29	rectum
43	chr12:49760000-49760200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr12:49760000-49760200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr12:49760000-49760200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
46	chr12:49760000-49760200	Flanking Active TSS	Primary T cells from cord blood	blood
47	chr12:49760000-49760200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
48	chr12:49760000-49760200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr12:49760000-49760200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
50	chr12:49760000-49760200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood

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