Variant report

Variant	rs699032
Chromosome Location	chr12:25151127-25151128
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	TBP	chr12:25150239-25151602	GM12878	blood:	n/a	n/a
2	MYC	chr12:25150937-25151637	MCF10A-Er-Src	breast:	n/a	chr12:25151313-25151326
3	POLR2A	chr12:25150932-25151480	HUVEC	blood vessel:	n/a	n/a
4	NFE2	chr12:25150976-25151431	GM12878	blood:	n/a	n/a
5	PAX5	chr12:25151061-25151463	GM12878	blood:	n/a	chr12:25151070-25151079
6	ATF2	chr12:25150550-25151595	GM12878	blood:	n/a	n/a
7	TBL1XR1	chr12:25150258-25151566	GM12878	blood:	n/a	n/a
8	IRF3	chr12:25150467-25151302	GM12878	blood:	n/a	n/a
9	RUNX3	chr12:25150193-25151589	GM12878	blood:	n/a	chr12:25151293-25151310
10	SP1	chr12:25150898-25151463	GM12878	blood:	n/a	n/a
11	CHD1	chr12:25150266-25151684	GM12878	blood:	n/a	n/a
12	FOS	chr12:25150947-25151326	MCF10A-Er-Src	breast:	n/a	n/a
13	MTA3	chr12:25150183-25151551	GM12878	blood:	n/a	n/a
14	POLR2A	chr12:25151024-25151224	MCF10A-Er-Src	breast:	n/a	n/a
15	BHLHE40	chr12:25150898-25151630	GM12878	blood:	n/a	n/a
16	POLR2A	chr12:25148411-25151968	GM12891	blood:	n/a	n/a
17	EP300	chr12:25150462-25151608	SK-N-SH_RA	brain:	n/a	chr12:25151065-25151079
18	NFATC1	chr12:25150531-25151671	GM12878	blood:	n/a	n/a
19	REST	chr12:25150979-25151336	GM12878	blood:	n/a	n/a
20	ZNF384	chr12:25150944-25151401	GM12878	blood:	n/a	n/a
21	EBF1	chr12:25151013-25151396	GM12878	blood:	n/a	n/a
22	FOS	chr12:25150934-25151339	MCF10A-Er-Src	breast:	n/a	n/a
23	NFIC	chr12:25150341-25151872	GM12878	blood:	n/a	n/a
24	MYC	chr12:25150982-25151273	MCF10A-Er-Src	breast:	n/a	n/a
25	USF1	chr12:25151111-25151401	SK-N-SH_RA	brain:	n/a	n/a
26	NFATC1	chr12:25150657-25151544	GM12878	blood:	n/a	n/a
27	EP300	chr12:25150455-25151635	SK-N-SH_RA	brain:	n/a	chr12:25151065-25151079
28	MEF2C	chr12:25150891-25151370	GM12878	blood:	n/a	chr12:25151112-25151126 chr12:25151179-25151190 chr12:25151113-25151124
29	FOSL2	chr12:25150929-25151373	SK-N-SH	brain:	n/a	n/a
30	PBX3	chr12:25150772-25151551	SK-N-SH	brain:	n/a	n/a
31	STAT3	chr12:25151040-25151276	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr12:25148336-25151602	GM12878	blood:	n/a	n/a
33	MEF2C	chr12:25150730-25151613	GM12878	blood:	n/a	chr12:25151112-25151126 chr12:25151179-25151190 chr12:25151113-25151124
34	NFIC	chr12:25150178-25151768	GM12878	blood:	n/a	n/a
35	STAT1	chr12:25150758-25151360	GM12878	blood:	n/a	n/a
36	IKZF1	chr12:25150452-25151611	GM12878	blood:	n/a	chr12:25151497-25151509
37	GATA3	chr12:25150607-25151789	SK-N-SH	brain:	n/a	chr12:25150648-25150655
38	BCL11A	chr12:25150977-25151346	GM12878	blood:	n/a	chr12:25151070-25151079
39	PBX3	chr12:25150630-25151760	SK-N-SH	brain:	n/a	n/a
40	MAFK	chr12:25151056-25151447	IMR90	lung:	n/a	n/a
41	RCOR1	chr12:25150314-25151597	GM12878	blood:	n/a	n/a
42	STAT5A	chr12:25150247-25151668	GM12878	blood:	n/a	n/a
43	POU2F2	chr12:25150834-25151494	GM12878	blood:	n/a	chr12:25151235-25151256 chr12:25150887-25150909
44	BCLAF1	chr12:25150815-25151670	GM12878	blood:	n/a	chr12:25151070-25151079
45	PAX5	chr12:25151031-25151378	GM12891	blood:	n/a	chr12:25151070-25151079
46	EP300	chr12:25150763-25151372	SK-N-SH	brain:	n/a	chr12:25151065-25151079
47	STAT3	chr12:25150446-25151390	GM12878	blood:	n/a	n/a
48	TCF12	chr12:25150589-25151628	SK-N-SH	brain:	n/a	n/a
49	FOXM1	chr12:25150234-25151627	GM12878	blood:	n/a	n/a
50	PML	chr12:25150840-25151408	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
C12orf77	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11047737	0.87[EUR][1000 genomes]
rs11047744	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11047746	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12227003	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12229477	0.83[EUR][1000 genomes]
rs17376659	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs34076340	1.00[ASN][1000 genomes]
rs34642683	0.81[EUR][1000 genomes]
rs67372216	1.00[ASN][1000 genomes]
rs699033	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs699035	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73061885	1.00[ASN][1000 genomes]
rs859135	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs859136	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs859145	0.84[GIH][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.96[MKK][hapmap];0.82[TSI][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs863490	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422312	chr12:24519392-25221686	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv469169	chr12:24692383-25357680	Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv557775	chr12:24692383-25357680	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv932477	chr12:24705151-25346677	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv1067577	chr12:24791283-25346677	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv529514	chr12:24791283-25346677	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers 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	22 gene(s)	inside rSNPs	diseases
7	nsv1041221	chr12:24880443-25213168	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv541425	chr12:24880443-25213168	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv469170	chr12:24891175-25204353	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv557776	chr12:24891175-25204353	Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
11	nsv557777	chr12:24891175-25205241	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
12	nsv469173	chr12:24891175-25207653	Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
13	nsv557778	chr12:24891175-25207653	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
14	nsv1049138	chr12:24921100-25164524	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
15	nsv1051319	chr12:24921100-25238936	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
16	nsv1037288	chr12:24941350-25238936	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
17	nsv541428	chr12:24941350-25238936	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
18	nsv1041218	chr12:24972019-25304356	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
19	esv3378403	chr12:25084023-25181017	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
20	nsv898921	chr12:25106961-25184896	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
21	nsv469174	chr12:25129015-25157129	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
22	nsv557795	chr12:25129015-25157129	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs699032	CASC1	cis	parietal	SCAN
rs699032	LRMP	Cis_1M	lymphoblastoid	RTeQTL
rs699032	ITPR2	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25141000-25152000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:25149800-25151600	Enhancers	Thymus	Thymus
3	chr12:25150200-25152000	Enhancers	HSMMtube	muscle
4	chr12:25150200-25152200	Enhancers	HSMM	muscle
5	chr12:25150400-25151200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr12:25150400-25151200	Flanking Active TSS	Primary B cells from peripheral blood	blood
7	chr12:25150400-25151200	Enhancers	Brain Hippocampus Middle	brain
8	chr12:25150400-25151200	Enhancers	Rectal Smooth Muscle	rectum
9	chr12:25150400-25151400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr12:25150400-25151400	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr12:25150400-25151400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:25150400-25151600	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr12:25150400-25151600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:25150400-25151600	Enhancers	NHDF-Ad	bronchial
15	chr12:25150400-25151800	Enhancers	Rectal Mucosa Donor 29	rectum
16	chr12:25150400-25152000	Enhancers	Osteobl	bone
17	chr12:25150400-25152200	Enhancers	Fetal Lung	lung
18	chr12:25150600-25151200	Enhancers	NHEK	skin
19	chr12:25150600-25151200	Enhancers	NHLF	lung
20	chr12:25150600-25151400	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr12:25150600-25151400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr12:25150600-25151400	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr12:25150600-25151600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr12:25150600-25151800	Enhancers	HUVEC	blood vessel
25	chr12:25150600-25152400	Enhancers	Colon Smooth Muscle	Colon
26	chr12:25150800-25151200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:25150800-25151400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr12:25150800-25151400	Enhancers	Fetal Heart	heart
29	chr12:25150800-25151600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:25150800-25151600	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr12:25150800-25151600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr12:25150800-25151600	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr12:25150800-25151600	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr12:25150800-25151800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
35	chr12:25150800-25154200	Weak transcription	Fetal Thymus	thymus
36	chr12:25151000-25151400	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr12:25151000-25151400	Enhancers	Stomach Smooth Muscle	stomach
38	chr12:25151000-25151400	Active TSS	GM12878-XiMat	blood
39	chr12:25151000-25151400	Enhancers	NH-A	brain
40	chr12:25151000-25151600	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr12:25151000-25151600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr12:25151000-25151600	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr12:25151000-25151600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
44	chr12:25151000-25151600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr12:25151000-25151600	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr12:25151000-25151600	Enhancers	Fetal Kidney	kidney
47	chr12:25151000-25151800	Enhancers	Dnd41	blood
48	chr12:25151000-25152400	Enhancers	Primary hematopoietic stem cells	blood

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