Variant report

Variant	rs41291959
Chromosome Location	chr12:48513027-48513028
allele	A/C
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	YY1	chr12:48512737-48513380	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr12:48512760-48513384	HEK293	kidney:	n/a	n/a
3	POLR2A	chr12:48512759-48513106	GM12891	blood:	n/a	n/a
4	POLR2A	chr12:48512741-48513993	MCF10A-Er-Src	breast:	n/a	n/a
5	MXI1	chr12:48512942-48513843	H1-hESC	embryonic stem cell:	n/a	n/a
6	TAF1	chr12:48512979-48513423	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAFK	chr12:48512441-48514143	Hela-S3	cervix:	n/a	chr12:48513708-48513724 chr12:48513711-48513725
8	SP4	chr12:48512908-48513385	H1-hESC	embryonic stem cell:	n/a	n/a
9	NRF1	chr12:48512817-48513288	GM12878	blood:	n/a	n/a
10	POLR2A	chr12:48513023-48513461	H1-hESC	embryonic stem cell:	n/a	n/a
11	TCF12	chr12:48512691-48513691	A549	lung:	n/a	n/a
12	POLR2A	chr12:48512813-48513479	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr12:48512716-48513393	HCT-116	colon:	n/a	n/a
14	TAF1	chr12:48512742-48513493	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr12:48512730-48513296	GM12892	blood:	n/a	n/a
16	YY1	chr12:48512743-48513397	ECC-1	luminal epithelium:	n/a	n/a
17	BHLHE40	chr12:48512819-48513812	GM12878	blood:	n/a	n/a
18	CCNT2	chr12:48512931-48513323	K562	blood:	n/a	n/a
19	MAZ	chr12:48512775-48513809	Hela-S3	cervix:	n/a	chr12:48513547-48513555
20	NFYB	chr12:48512895-48513148	GM12878	blood:	n/a	n/a
21	YY1	chr12:48512738-48513315	SK-N-SH_RA	brain:	n/a	n/a
22	IRF1	chr12:48512739-48513292	K562	blood:	n/a	chr12:48513272-48513286 chr12:48513272-48513282
23	TCF12	chr12:48512777-48513630	ECC-1	luminal epithelium:	n/a	n/a
24	MAX	chr12:48512895-48513823	SK-N-SH	brain:	n/a	chr12:48513547-48513555
25	ZNF143	chr12:48512886-48513334	GM12878	blood:	n/a	chr12:48512927-48512945
26	POLR2A	chr12:48512672-48513421	SK-N-SH	brain:	n/a	n/a
27	STAT3	chr12:48512981-48513144	MCF10A-Er-Src	breast:	n/a	n/a
28	TBP	chr12:48512342-48513566	H1-hESC	embryonic stem cell:	n/a	n/a
29	MAZ	chr12:48512366-48513603	K562	blood:	n/a	chr12:48513547-48513555
30	ELF1	chr12:48512815-48513438	GM12878	blood:	n/a	chr12:48512983-48512996
31	POLR2A	chr12:48512690-48513357	U87	brain:	n/a	n/a
32	TAF1	chr12:48512787-48513421	PFSK-1	brain:	n/a	n/a
33	TAF1	chr12:48512771-48513333	Hela-S3	cervix:	n/a	n/a
34	MAX	chr12:48512869-48513845	A549	lung:	n/a	chr12:48513547-48513555
35	MAX	chr12:48513003-48513251	K562	blood:	n/a	n/a
36	TBP	chr12:48512231-48514177	Hela-S3	cervix:	n/a	n/a
37	YY1	chr12:48512727-48513247	SK-N-SH_RA	brain:	n/a	n/a
38	MYC	chr12:48512901-48513819	K562	blood:	n/a	chr12:48513547-48513555
39	TAF1	chr12:48512871-48513294	PFSK-1	brain:	n/a	n/a
40	YY1	chr12:48512844-48513283	HCT-116	colon:	n/a	n/a
41	POLR2A	chr12:48512857-48513364	A549	lung:	n/a	n/a
42	POLR2A	chr12:48512888-48513366	ProgFib	skin:	n/a	n/a
43	TBL1XR1	chr12:48512953-48513357	GM12878	blood:	n/a	n/a
44	MAX	chr12:48512854-48513793	Hela-S3	cervix:	n/a	chr12:48513547-48513555
45	POLR2A	chr12:48512629-48513589	PFSK-1	brain:	n/a	n/a
46	MAX	chr12:48512928-48513712	K562	blood:	n/a	chr12:48513547-48513555
47	POLR2A	chr12:48512882-48513265	A549	lung:	n/a	n/a
48	POLR2A	chr12:48512760-48513734	H1-neurons	neurons:	n/a	n/a
49	POLR2A	chr12:48512708-48513357	U87	brain:	n/a	n/a
50	POLR2A	chr12:48512832-48513398	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48497262..48501671-chr12:48511273..48513832,5	K562	blood:
2	chr12:48511519..48514886-chr12:48548320..48552889,5	K562	blood:
3	chr12:48496389..48500489-chr12:48511491..48515053,4	K562	blood:
4	chr12:48498567..48501846-chr12:48512929..48518601,8	MCF-7	breast:
5	chr12:48497586..48502171-chr12:48511099..48514258,8	MCF-7	breast:
6	chr12:48510785..48513717-chr12:48592045..48593630,2	K562	blood:
7	chr12:48511276..48513909-chr12:48515822..48517335,2	K562	blood:

Variant related genes	Relation type
PFKM	TF binding region
ENSG00000079387	Chromatin interaction
ENSG00000152556	Chromatin interaction
ENSG00000177981	Chromatin interaction
ENSG00000269514	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1004746	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1004806	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10506277	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12301562	0.86[EUR][1000 genomes]
rs17224674	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17225261	0.89[AMR][1000 genomes]
rs17225366	0.89[AMR][1000 genomes]
rs17225751	0.89[AMR][1000 genomes]
rs17607800	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs17824200	0.89[AMR][1000 genomes]
rs2228501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3936179	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4075914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41291961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55682541	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55707383	0.87[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs55752728	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55794326	0.89[AMR][1000 genomes]
rs55820056	0.82[EUR][1000 genomes]
rs55886138	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55890195	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55894137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55945889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55953382	0.87[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs56049209	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56116946	0.89[AMR][1000 genomes]
rs56187356	0.89[EUR][1000 genomes]
rs56205628	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56288528	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56378908	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60209369	0.86[EUR][1000 genomes]
rs74089155	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41291959	ZNF641	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48512400-48513800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr12:48512400-48513800	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr12:48512400-48514000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr12:48512400-48514000	Active TSS	Brain Anterior Caudate	brain
5	chr12:48512400-48514200	Active TSS	Ovary	ovary
6	chr12:48512400-48514400	Active TSS	Stomach Smooth Muscle	stomach
7	chr12:48512400-48514600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr12:48512400-48514800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr12:48512400-48515400	Active TSS	Brain Angular Gyrus	brain
10	chr12:48512600-48513200	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr12:48512600-48513200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
12	chr12:48512600-48513200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
13	chr12:48512600-48513400	Flanking Active TSS	Thymus	Thymus
14	chr12:48512600-48513400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr12:48512600-48513600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr12:48512600-48513600	Active TSS	Brain Substantia Nigra	brain
17	chr12:48512600-48513600	Active TSS	Fetal Intestine Small	intestine
18	chr12:48512600-48513600	Active TSS	Stomach Mucosa	stomach
19	chr12:48512600-48513600	Active TSS	NH-A	brain
20	chr12:48512600-48513800	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr12:48512600-48513800	Active TSS	Colonic Mucosa	Colon
22	chr12:48512600-48513800	Active TSS	Rectal Mucosa Donor 29	rectum
23	chr12:48512600-48514000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:48512600-48514000	Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr12:48512600-48514000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:48512600-48514000	Active TSS	Brain Germinal Matrix	brain
27	chr12:48512600-48514000	Active TSS	Fetal Intestine Large	intestine
28	chr12:48512600-48514000	Active TSS	Fetal Kidney	kidney
29	chr12:48512600-48514000	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr12:48512600-48514000	Active TSS	Placenta	Placenta
31	chr12:48512600-48514200	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr12:48512600-48514200	Active TSS	H1 Cell Line	embryonic stem cell
33	chr12:48512600-48514200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:48512600-48514200	Active TSS	Brain Cingulate Gyrus	brain
35	chr12:48512600-48514200	Active TSS	Brain Inferior Temporal Lobe	brain
36	chr12:48512600-48514200	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr12:48512600-48514200	Active TSS	NHDF-Ad	bronchial
38	chr12:48512600-48514600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr12:48512600-48516400	Active TSS	Right Atrium	heart
40	chr12:48512800-48513200	Flanking Active TSS	Primary B cells from peripheral blood	blood
41	chr12:48512800-48513200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
42	chr12:48512800-48513400	Active TSS	Duodenum Mucosa	Duodenum
43	chr12:48512800-48513400	Flanking Active TSS	Lung	lung
44	chr12:48512800-48513600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
45	chr12:48512800-48513600	Active TSS	Primary B cells from cord blood	blood
46	chr12:48512800-48513600	Active TSS	Primary T cells from cord blood	blood
47	chr12:48512800-48513600	Active TSS	Primary T helper naive cells from peripheral blood	blood
48	chr12:48512800-48513600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
49	chr12:48512800-48513600	Active TSS	Colon Smooth Muscle	Colon
50	chr12:48512800-48513600	Active TSS	Fetal Lung	lung

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