Variant report

Variant	rs17123790
Chromosome Location	chr12:49961966-49961967
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	TAL1	chr12:49961618-49961983	K562	blood:	n/a	n/a
2	TCF12	chr12:49961629-49962179	A549	lung:	n/a	n/a
3	ELF1	chr12:49961630-49962158	HepG2	liver:	n/a	chr12:49961915-49961926 chr12:49961914-49961927 chr12:49961916-49961925 chr12:49961915-49961926
4	POLR2A	chr12:49961396-49962408	HCT-116	colon:	n/a	n/a
5	CEBPD	chr12:49961750-49962041	HepG2	liver:	n/a	n/a
6	POLR2A	chr12:49961202-49962575	Hela-S3	cervix:	n/a	n/a
7	RELA	chr12:49961448-49962368	GM15510	blood:	n/a	n/a
8	POU2F2	chr12:49961619-49962223	GM12891	blood:	n/a	n/a
9	KAP1	chr12:49961750-49962620	U2OS	brain:	n/a	n/a
10	TBP	chr12:49961437-49962390	Hela-S3	cervix:	n/a	n/a
11	SIN3AK20	chr12:49961742-49962397	PFSK-1	brain:	n/a	n/a
12	MXI1	chr12:49961276-49962815	GM12878	blood:	n/a	chr12:49961955-49961970
13	RCOR1	chr12:49961219-49962220	Hela-S3	cervix:	n/a	n/a
14	TAF1	chr12:49961601-49962097	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr12:49961371-49962139	GM12891	blood:	n/a	n/a
16	POLR2A	chr12:49961363-49962274	HepG2	liver:	n/a	n/a
17	POLR2A	chr12:49961399-49962181	HepG2	liver:	n/a	n/a
18	MAX	chr12:49961467-49962538	NB4	blood:	n/a	n/a
19	CREB1	chr12:49961377-49962261	HepG2	liver:	n/a	chr12:49961519-49961532
20	SIN3AK20	chr12:49961773-49962372	K562	blood:	n/a	n/a
21	NR2C2	chr12:49961285-49962221	GM12878	blood:	n/a	n/a
22	SIN3AK20	chr12:49961690-49962231	H1-hESC	embryonic stem cell:	n/a	n/a
23	JUND	chr12:49961343-49962139	A549	lung:	n/a	n/a
24	POLR2A	chr12:49961220-49962478	SK-N-SH	brain:	n/a	n/a
25	TCF12	chr12:49961171-49962494	ECC-1	luminal epithelium:	n/a	n/a
26	USF2	chr12:49961847-49962138	HepG2	liver:	n/a	n/a
27	POLR2A	chr12:49961225-49962381	U87	brain:	n/a	n/a
28	POLR2A	chr12:49961286-49962047	GM12878	blood:	n/a	n/a
29	SIN3AK20	chr12:49961633-49962599	H1-hESC	embryonic stem cell:	n/a	n/a
30	ZKSCAN1	chr12:49961252-49962225	Hela-S3	cervix:	n/a	n/a
31	RCOR1	chr12:49961475-49962333	K562	blood:	n/a	n/a
32	POLR2A	chr12:49961456-49962184	MCF-7	breast:	n/a	n/a
33	ETS1	chr12:49961379-49962399	A549	lung:	n/a	chr12:49961915-49961924 chr12:49961915-49961924 chr12:49961914-49961927 chr12:49961915-49961924 chr12:49961915-49961924 chr12:49961915-49961924 chr12:49961915-49961924 chr12:49961949-49961958 chr12:49961912-49961928 chr12:49961916-49961925 chr12:49961915-49961924 chr12:49962339-49962352 chr12:49961950-49961959 chr12:49961913-49961923
34	POLR2A	chr12:49961446-49962192	HepG2	liver:	n/a	n/a
35	RELA	chr12:49961292-49962318	GM18951	blood:	n/a	n/a
36	POLR2A	chr12:49961397-49962434	GM12878	blood:	n/a	n/a
37	TBL1XR1	chr12:49961390-49962381	K562	blood:	n/a	n/a
38	POLR2A	chr12:49961126-49962517	K562	blood:	n/a	n/a
39	YY1	chr12:49961417-49962101	SK-N-SH_RA	brain:	n/a	n/a
40	MXI1	chr12:49961491-49962458	H1-hESC	embryonic stem cell:	n/a	chr12:49961955-49961970
41	ZBTB33	chr12:49961471-49962134	A549	lung:	n/a	n/a
42	MAX	chr12:49961285-49962806	Hela-S3	cervix:	n/a	n/a
43	MYC	chr12:49961719-49962447	K562	blood:	n/a	n/a
44	NFIC	chr12:49961691-49962236	HepG2	liver:	n/a	n/a
45	SP1	chr12:49961690-49962085	GM12878	blood:	n/a	chr12:49961721-49961730 chr12:49961719-49961731 chr12:49961979-49961991 chr12:49961721-49961730 chr12:49961979-49961991 chr12:49961980-49961990 chr12:49961720-49961730 chr12:49961980-49961990 chr12:49961719-49961731 chr12:49961720-49961729
46	POLR2A	chr12:49961398-49962076	GM12891	blood:	n/a	n/a
47	NRF1	chr12:49961242-49962084	GM12878	blood:	n/a	chr12:49961688-49961702 chr12:49961691-49961705 chr12:49961646-49961657 chr12:49961693-49961702 chr12:49961691-49961702 chr12:49961646-49961655 chr12:49961691-49961702 chr12:49961643-49961657 chr12:49961646-49961660 chr12:49961645-49961656
48	GABPA	chr12:49961206-49962545	SK-N-SH	brain:	n/a	chr12:49961688-49961702 chr12:49961691-49961705 chr12:49961646-49961657 chr12:49961693-49961702 chr12:49961691-49961702 chr12:49961646-49961655 chr12:49961643-49961657 chr12:49961646-49961660
49	POLR2A	chr12:49961418-49962473	Raji	blood:	n/a	n/a
50	POLR2A	chr12:49961479-49962058	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:49961921-49961971	NB4	blood:	n/a
2	chr12:49961959-49962009	CMK	blood:	n/a
3	chr12:49961959-49962009	NH-A	brain:	n/a
4	chr12:49961959-49962009	AG10803	skin:	n/a
5	chr12:49961959-49962009	SK-N-SH	brain:	n/a
6	chr12:49961959-49962009	LNCaP	prostate:	n/a
7	chr12:49961921-49961971	GM19239	blood:	n/a
8	chr12:49961921-49961971	HMEC	breast:	n/a
9	chr12:49961921-49961971	PANC-1	pancreas:	n/a
10	chr12:49961959-49962009	BE2_C	brain:	n/a
11	chr12:49961959-49962009	PrEC	prostate:	n/a
12	chr12:49961921-49961971	GM12878	blood:	n/a
13	chr12:49961959-49962009	HAEpiC	amniotic membrane:	n/a
14	chr12:49961921-49961971	Caco-2	colon:	n/a
15	chr12:49961959-49962009	HCF	heart:	n/a
16	chr12:49961959-49962009	HepG2	liver:	n/a
17	chr12:49961921-49961971	HCM	heart:	n/a
18	chr12:49961921-49961971	A549	lung:	n/a
19	chr12:49961921-49961971	BJ	skin:	n/a
20	chr12:49961959-49962009	NHBE	bronchial:	n/a
21	chr12:49961959-49962009	HEK293	kidney:	embryo
22	chr12:49961959-49962009	HCT-116	colon:	n/a
23	chr12:49961959-49962009	RPTEC	kidney:	n/a
24	chr12:49961959-49962009	NHDF-neo	bronchial:	n/a
25	chr12:49961959-49962009	AoSMC	blood vessel:	n/a
26	chr12:49961959-49962009	U87	brain:	n/a
27	chr12:49961921-49961971	MCF-7	breast:	n/a
28	chr12:49961921-49961971	HUVEC	blood vessel:	n/a
29	chr12:49961921-49961971	SAEC	small airway:	n/a
30	chr12:49961959-49962009	HUVEC	blood vessel:	n/a
31	chr12:49961921-49961971	GM06990	blood:	n/a
32	chr12:49961959-49962009	HNPCEpiC	eye:	n/a
33	chr12:49961921-49961971	ECC-1	luminal epithelium:	n/a
34	chr12:49961959-49962009	AG09319	gingival:	n/a
35	chr12:49961959-49962009	HIPEpiC	eye:	n/a
36	chr12:49961921-49961971	HIPEpiC	eye:	n/a
37	chr12:49961921-49961971	HRE	kidney:	n/a
38	chr12:49961921-49961971	AG04449	skin:	fetal
39	chr12:49961959-49962009	PFSK-1	brain:	n/a
40	chr12:49961921-49961971	GM12892	blood:	n/a
41	chr12:49961959-49962009	AG09309	skin:	n/a
42	chr12:49961959-49962009	GM12878	blood:	n/a
43	chr12:49961921-49961971	SK-N-MC	brain:	n/a
44	chr12:49961921-49961971	AG10803	skin:	n/a
45	chr12:49961921-49961971	SK-N-SH	brain:	n/a
46	chr12:49961921-49961971	AoSMC	blood vessel:	n/a
47	chr12:49961959-49962009	Hela-S3	cervix:	n/a
48	chr12:49961921-49961971	BE2_C	brain:	n/a
49	chr12:49961921-49961971	NHBE	bronchial:	n/a
50	chr12:49961921-49961971	HCPEpiC	choroid plexus:	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:49960207..49964959-chr12:50014167..50018580,9	MCF-7	breast:
2	chr12:49737598..49740843-chr12:49959274..49963250,5	K562	blood:
3	chr12:49658339..49661093-chr12:49961458..49963113,2	MCF-7	breast:
4	chr12:49961495..49963376-chr12:50017073..50019331,3	MCF-7	breast:
5	chr12:49961142..49963123-chr12:50022315..50024397,2	K562	blood:
6	chr12:49716225..49717888-chr12:49960972..49962551,2	K562	blood:
7	chr12:49930865..49935032-chr12:49959689..49963246,5	K562	blood:
8	chr12:49740266..49744152-chr12:49960185..49963713,4	MCF-7	breast:
9	chr12:49961367..49962113-chr15:89877701..89878202,2	Hela-S3	cervix:
10	chr12:49759487..49762377-chr12:49960316..49963479,6	K562	blood:
11	chr12:49960315..49962480-chr12:49993322..49995583,2	MCF-7	breast:
12	chr12:49960870..49963498-chr12:50026021..50027997,2	K562	blood:
13	chr12:49960658..49962716-chr12:50235265..50237902,2	K562	blood:
14	chr12:49960831..49963371-chr12:50134082..50136909,3	K562	blood:
15	chr12:49961053..49963139-chr12:49984640..49987053,2	K562	blood:
16	chr12:49959993..49964620-chr12:49965374..49976382,20	MCF-7	breast:
17	chr12:49931420..49936579-chr12:49960006..49963071,6	MCF-7	breast:
18	chr12:49960687..49963976-chr12:50022315..50025513,4	K562	blood:
19	chr12:49958946..49963914-chr12:49967568..49975925,12	MCF-7	breast:
20	chr12:49523716..49526507-chr12:49960651..49963397,2	K562	blood:
21	chr12:49960372..49963252-chr12:50011944..50013920,2	MCF-7	breast:
22	chr12:49960473..49963349-chr12:50134082..50137265,4	K562	blood:
23	chr12:49759658..49762377-chr12:49960316..49963047,2	K562	blood:
24	chr12:49350125..49350994-chr12:49961421..49962193,2	Hela-S3	cervix:
25	chr12:49760076..49762481-chr12:49958970..49962083,4	MCF-7	breast:
26	chr12:49715809..49718434-chr12:49958773..49962472,3	K562	blood:

Variant related genes	Relation type
PRPF40B	TF binding region
MCRS1	TF binding region
MCRS1	CpG island
PRPF40B	CpG island
ENSG00000186666	Chromatin interaction
ENSG00000258104	Chromatin interaction
ENSG00000140521	Chromatin interaction
ENSG00000134287	Chromatin interaction
ENSG00000135436	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000199237	Chromatin interaction
ENSG00000139644	Chromatin interaction
ENSG00000257964	Chromatin interaction
ENSG00000135451	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000135519	Chromatin interaction
ENSG00000178401	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000258334	Chromatin interaction
ENSG00000110844	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000123352	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11169016	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11169048	1.00[CHB][hapmap]
rs11169058	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11169059	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11834161	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12296440	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12301632	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12305716	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12306118	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12309053	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12315996	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12322561	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17123751	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17123865	1.00[ASW][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap]
rs17123919	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs17123922	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs17123943	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[YRI][hapmap]
rs17197593	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272478	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4144469	1.00[JPT][hapmap]
rs4569075	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580707	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6580709	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6580716	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7139061	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7294648	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7294973	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7295162	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7342365	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7955541	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7962951	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7969099	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7976165	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9919739	0.83[AMR][1000 genomes]
rs9919740	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs9919807	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832406	chr12:49860693-50062136	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv482795	chr12:49897633-50068686	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 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	chr12:49960200-49963200	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr12:49960400-49962800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:49960600-49962800	Active TSS	Fetal Kidney	kidney
4	chr12:49960600-49963000	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr12:49960600-49963200	Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr12:49960800-49962800	Active TSS	Psoas Muscle	Psoas
7	chr12:49960800-49963000	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr12:49960800-49963000	Active TSS	H9 Cell Line	embryonic stem cell
9	chr12:49960800-49963000	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr12:49960800-49963000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr12:49960800-49963000	Flanking Active TSS	Primary hematopoietic stem cells	blood
12	chr12:49960800-49963000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr12:49960800-49963000	Active TSS	Right Atrium	heart
14	chr12:49960800-49963000	Active TSS	Right Ventricle	heart
15	chr12:49960800-49963200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr12:49960800-49963200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr12:49960800-49963200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr12:49961000-49962600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr12:49961000-49962600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr12:49961000-49962600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:49961000-49962600	Active TSS	Placenta Amnion	Placenta Amnion
22	chr12:49961000-49962600	Active TSS	NHEK	skin
23	chr12:49961000-49962800	Active TSS	H1 Cell Line	embryonic stem cell
24	chr12:49961000-49962800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:49961000-49962800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr12:49961000-49962800	Active TSS	Esophagus	oesophagus
27	chr12:49961000-49962800	Active TSS	Stomach Mucosa	stomach
28	chr12:49961000-49962800	Active TSS	HMEC	breast
29	chr12:49961000-49962800	Active TSS	NHDF-Ad	bronchial
30	chr12:49961000-49962800	Active TSS	NHLF	lung
31	chr12:49961000-49963000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr12:49961000-49963000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr12:49961000-49963000	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr12:49961000-49963000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr12:49961000-49963000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr12:49961000-49963000	Active TSS	Fetal Intestine Large	intestine
37	chr12:49961000-49963000	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr12:49961000-49963000	Active TSS	Ovary	ovary
39	chr12:49961000-49963000	Active TSS	HSMMtube	muscle
40	chr12:49961000-49963200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr12:49961000-49963200	Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr12:49961000-49963200	Active TSS	A549	lung
43	chr12:49961000-49963200	Active TSS	GM12878-XiMat	blood
44	chr12:49961000-49963200	Active TSS	HSMM	muscle
45	chr12:49961000-49963400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr12:49961000-49963600	Active TSS	K562	blood
47	chr12:49961200-49962400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
48	chr12:49961200-49962600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr12:49961200-49962600	Active TSS	Brain Hippocampus Middle	brain
50	chr12:49961200-49962600	Active TSS	Brain Inferior Temporal Lobe	brain

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