Variant report

Variant	rs61942052
Chromosome Location	chr12:49075983-49075984
allele	C/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	ZEB1	chr12:49075909-49076339	GM12878	blood:	n/a	n/a
2	MYC	chr12:49075459-49076468	K562	blood:	n/a	chr12:49075701-49075710
3	TAF1	chr12:49075136-49076400	GM12878	blood:	n/a	n/a
4	TAF1	chr12:49075233-49076574	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr12:49075069-49076494	GM12892	blood:	n/a	n/a
6	POLR2A	chr12:49075391-49076435	HCT-116	colon:	n/a	n/a
7	POLR2A	chr12:49075090-49076480	PBDE	blood:	n/a	n/a
8	POLR2A	chr12:49075126-49076286	GM12892	blood:	n/a	n/a
9	ELK1	chr12:49075764-49076342	Hela-S3	cervix:	n/a	n/a
10	MAX	chr12:49075421-49076501	MCF-7	breast:	n/a	chr12:49075701-49075710
11	TAF1	chr12:49075636-49076318	GM12891	blood:	n/a	n/a
12	YY1	chr12:49075322-49076458	SK-N-SH_RA	brain:	n/a	chr12:49075957-49075967 chr12:49075796-49075818 chr12:49075550-49075559 chr12:49075799-49075807 chr12:49075957-49075979 chr12:49075795-49075807 chr12:49075958-49075966
13	RFX5	chr12:49074994-49076566	SK-N-SH	brain:	n/a	chr12:49076072-49076081
14	E2F4	chr12:49075787-49076367	MCF10A-Er-Src	breast:	n/a	n/a
15	ZC3H11A	chr12:49075706-49076041	K562	blood:	n/a	n/a
16	YY1	chr12:49075356-49076397	ECC-1	luminal epithelium:	n/a	chr12:49075957-49075967 chr12:49075796-49075818 chr12:49075550-49075559 chr12:49075799-49075807 chr12:49075957-49075979 chr12:49075795-49075807 chr12:49075958-49075966
17	SP2	chr12:49075760-49076382	HepG2	liver:	n/a	chr12:49076046-49076055
18	CEBPB	chr12:49075828-49076339	Hela-S3	cervix:	n/a	chr12:49076073-49076081
19	POLR2A	chr12:49075294-49076547	MCF-7	breast:	n/a	n/a
20	E2F4	chr12:49075816-49076192	GM12878	blood:	n/a	n/a
21	MXI1	chr12:49075295-49076456	K562	blood:	n/a	n/a
22	POLR2A	chr12:49075563-49076569	PFSK-1	brain:	n/a	n/a
23	CTCF	chr12:49075981-49076169	Spleen_OC	spleen:	n/a	n/a
24	POLR2A	chr12:49075162-49076539	K562	blood:	n/a	n/a
25	MBD4	chr12:49075472-49076101	HepG2	liver:	n/a	n/a
26	POLR2A	chr12:49075029-49076470	MCF10A-Er-Src	breast:	n/a	n/a
27	YY1	chr12:49075172-49076261	H1-hESC	embryonic stem cell:	n/a	chr12:49075957-49075967 chr12:49075796-49075818 chr12:49075550-49075559 chr12:49075799-49075807 chr12:49075957-49075979 chr12:49075795-49075807 chr12:49075958-49075966
28	E2F4	chr12:49075335-49076302	K562	blood:	n/a	chr12:49075550-49075559
29	PML	chr12:49075578-49076327	MCF-7	breast:	n/a	n/a
30	POLR2A	chr12:49074942-49076456	K562	blood:	n/a	n/a
31	TBP	chr12:49075260-49076361	H1-hESC	embryonic stem cell:	n/a	n/a
32	MAX	chr12:49075128-49076508	SK-N-SH	brain:	n/a	chr12:49075701-49075710
33	MAFK	chr12:49075805-49076315	HepG2	liver:	n/a	chr12:49076187-49076202
34	TAL1	chr12:49075448-49076263	K562	blood:	n/a	n/a
35	BHLHE40	chr12:49075656-49076224	GM12878	blood:	n/a	n/a
36	SP2	chr12:49075858-49076298	K562	blood:	n/a	chr12:49076046-49076055
37	SIN3AK20	chr12:49075441-49076446	K562	blood:	n/a	n/a
38	CHD1	chr12:49075043-49076041	H1-hESC	embryonic stem cell:	n/a	n/a
39	HA-E2F1	chr12:49075647-49076242	Hela-S3	cervix:	n/a	n/a
40	TAF1	chr12:49075343-49076446	K562	blood:	n/a	n/a
41	ATF2	chr12:49075519-49076104	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr12:49075431-49076368	HUVEC	blood vessel:	n/a	n/a
43	EP300	chr12:49075738-49076163	HepG2	liver:	n/a	chr12:49075974-49075990
44	REST	chr12:49075680-49076387	HepG2	liver:	n/a	n/a
45	TAF1	chr12:49075325-49076485	ECC-1	luminal epithelium:	n/a	n/a
46	CBX3	chr12:49075516-49076511	K562	blood:	n/a	n/a
47	ZNF263	chr12:49075229-49076186	HEK293-T-REx	kidney:	n/a	n/a
48	BCL3	chr12:49075494-49076352	A549	lung:	n/a	chr12:49075550-49075563 chr12:49075998-49076011
49	REST	chr12:49075549-49076190	SK-N-SH	brain:	n/a	n/a
50	BRCA1	chr12:49075804-49076209	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:49075230..49077849-chr12:49244507..49246836,3	MCF-7	breast:
2	chr12:49073658..49078597-chr12:49201352..49212442,12	MCF-7	breast:
3	chr12:49074389..49076545-chr12:49180456..49183753,3	MCF-7	breast:
4	chr12:49074245..49078609-chr12:49180778..49182867,4	MCF-7	breast:
5	chr12:49075515..49076182-chr7:100209563..100210466,2	Hela-S3	cervix:
6	chr12:49072667..49077768-chr12:49107571..49112359,8	MCF-7	breast:
7	chr12:49072707..49077771-chr12:49103757..49111723,15	MCF-7	breast:
8	chr12:49075600..49076194-chr19:16940082..16940653,2	Hela-S3	cervix:
9	chr1:117907595..117908581-chr12:49075347..49076268,2	MCF-7	breast:
10	chr12:49075418..49076068-chr3:36949235..36950020,2	NB4	blood:
11	chr1:211555799..211556573-chr12:49075458..49076102,2	Hela-S3	cervix:
12	chr12:49052583..49059422-chr12:49071692..49076510,9	K562	blood:
13	chr12:49073851..49077506-chr12:49084529..49091835,9	MCF-7	breast:
14	chr12:49074430..49078671-chr12:49171491..49175460,5	MCF-7	breast:
15	chr12:49075682..49076266-chr17:26988965..26989517,2	Hela-S3	cervix:
16	chr12:49075684..49076658-chr16:74808184..74809111,2	Hela-S3	cervix:
17	chr12:49075625..49076327-chr15:75917685..75918191,2	Hela-S3	cervix:
18	chr12:49052650..49057544-chr12:49071692..49076123,6	K562	blood:
19	chr12:49075477..49077104-chr16:57653013..57654858,2	MCF-7	breast:
20	chr12:49072639..49079132-chr12:49108469..49112073,12	K562	blood:
21	chr12:49075486..49077748-chr12:49208337..49210735,3	K562	blood:
22	chr12:49075559..49076382-chr9:130341183..130341702,2	Hela-S3	cervix:
23	chr12:49073439..49079132-chr12:49108039..49112179,15	K562	blood:
24	chr12:49075650..49076266-chr5:72251743..72252318,2	Hela-S3	cervix:
25	chr12:49075639..49076241-chr8:42195484..42196293,2	NB4	blood:
26	chr12:49075769..49076744-chr17:56405737..56406693,2	NB4	blood:

Variant related genes	Relation type
KANSL2	TF binding region
ENSG00000168016	Chromatin interaction
ENSG00000103089	Chromatin interaction
ENSG00000167535	Chromatin interaction
ENSG00000005379	Chromatin interaction
ENSG00000106330	Chromatin interaction
ENSG00000169371	Chromatin interaction
ENSG00000265148	Chromatin interaction
ENSG00000174233	Chromatin interaction
ENSG00000153363	Chromatin interaction
ENSG00000132581	Chromatin interaction
ENSG00000157107	Chromatin interaction
ENSG00000139620	Chromatin interaction
ENSG00000257660	Chromatin interaction
ENSG00000127511	Chromatin interaction
ENSG00000205336	Chromatin interaction
ENSG00000129315	Chromatin interaction
ENSG00000109111	Chromatin interaction
ENSG00000070501	Chromatin interaction
ENSG00000271427	Chromatin interaction
ENSG00000174243	Chromatin interaction
ENSG00000136830	Chromatin interaction
ENSG00000207467	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10875851	0.81[AMR][1000 genomes]
rs11168659	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11168660	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11168661	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11168664	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11168667	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11168680	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11168690	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11168691	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11168692	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11168693	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11168694	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11168695	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11168699	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11168700	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11168701	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11168708	0.87[AFR][1000 genomes]
rs11832160	0.81[AMR][1000 genomes]
rs12366919	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17834622	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1895994	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2409084	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3013	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4132370	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61942011	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61942012	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61942013	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61942014	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61942015	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61942016	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61942018	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61942047	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61942048	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61942049	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61942051	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61942053	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61942058	0.92[EUR][1000 genomes]
rs61942059	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6580694	0.87[AFR][1000 genomes]
rs7294389	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7295027	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7295138	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7303113	0.81[AMR][1000 genomes]
rs7486636	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7964801	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7966343	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7967175	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7967542	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7973954	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7979508	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][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	esv3332169	chr12:49005807-49150691	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
2	nsv519053	chr12:49065727-49079470	Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	24 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49074200-49076600	Active TSS	H9 Cell Line	embryonic stem cell
2	chr12:49074200-49076600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr12:49074200-49076800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr12:49074400-49076600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr12:49074400-49076600	Active TSS	HSMM	muscle
6	chr12:49074400-49076600	Active TSS	NHLF	lung
7	chr12:49074400-49076800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:49074400-49076800	Active TSS	A549	lung
9	chr12:49074400-49076800	Active TSS	HMEC	breast
10	chr12:49074400-49077000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:49074400-49077000	Active TSS	K562	blood
12	chr12:49074600-49076600	Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr12:49074600-49076600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr12:49074600-49076600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr12:49074600-49076800	Active TSS	H1 Cell Line	embryonic stem cell
16	chr12:49074600-49076800	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr12:49074600-49076800	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr12:49074600-49076800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr12:49074600-49076800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:49074600-49076800	Active TSS	Stomach Smooth Muscle	stomach
21	chr12:49074600-49077000	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr12:49074600-49077000	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr12:49074600-49077200	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr12:49074800-49076600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:49074800-49076600	Active TSS	Muscle Satellite Cultured Cells	--
26	chr12:49074800-49076600	Active TSS	Aorta	Aorta
27	chr12:49074800-49076600	Active TSS	Fetal Kidney	kidney
28	chr12:49074800-49076600	Active TSS	Left Ventricle	heart
29	chr12:49074800-49076600	Active TSS	Ovary	ovary
30	chr12:49074800-49076600	Active TSS	Pancreas	Pancrea
31	chr12:49074800-49076600	Active TSS	Rectal Smooth Muscle	rectum
32	chr12:49074800-49076800	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr12:49074800-49076800	Active TSS	Primary T helper cells PMA-I stimulated	--
34	chr12:49074800-49076800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr12:49074800-49076800	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr12:49074800-49076800	Active TSS	Fetal Brain Female	brain
37	chr12:49074800-49076800	Active TSS	Hela-S3	cervix
38	chr12:49074800-49077000	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr12:49074800-49077000	Active TSS	Pancreatic Islets	Pancreatic Islet
40	chr12:49074800-49077000	Active TSS	Right Ventricle	heart
41	chr12:49074800-49077200	Active TSS	Rectal Mucosa Donor 29	rectum
42	chr12:49074800-49077200	Active TSS	GM12878-XiMat	blood
43	chr12:49075000-49076000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
44	chr12:49075000-49076000	Active TSS	Stomach Mucosa	stomach
45	chr12:49075000-49076400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
46	chr12:49075000-49076400	Active TSS	Fetal Heart	heart
47	chr12:49075000-49076600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr12:49075000-49076600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:49075000-49076600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr12:49075000-49076600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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