Variant report

Variant	rs12818777
Chromosome Location	chr12:59990069-59990070
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	POLR2A	chr12:59989388-59991554	GM12892	blood:	n/a	n/a
2	MYC	chr12:59989184-59991670	NB4	blood:	n/a	chr12:59990810-59990825
3	CTCF	chr12:59989960-59990110	HRE	kidney:	n/a	n/a
4	CTCF	chr12:59989940-59990090	GM12866	blood:	n/a	n/a
5	POLR2A	chr12:59989990-59990199	GM12891	blood:	n/a	n/a
6	CTCF	chr12:59989959-59990076	Fibrobl	skin:	n/a	n/a
7	POLR2A	chr12:59989734-59991087	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr12:59989531-59991141	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr12:59989341-59991607	Raji	blood:	n/a	n/a
10	POLR2A	chr12:59989748-59991058	Hela-S3	cervix:	n/a	n/a
11	CTCF	chr12:59989920-59990070	GM12870	blood:	n/a	n/a
12	CHD2	chr12:59989937-59991017	H1-hESC	embryonic stem cell:	n/a	n/a
13	SRF	chr12:59990052-59990353	H1-hESC	embryonic stem cell:	n/a	chr12:59990185-59990196 chr12:59990184-59990198 chr12:59990184-59990199
14	CTCF	chr12:59989920-59990070	HAc	cerebellar:	n/a	n/a
15	POLR2A	chr12:59989314-59991660	GM12878	blood:	n/a	n/a
16	CTCF	chr12:59989896-59990088	H1-hESC	embryonic stem cell:	n/a	n/a
17	TAF1	chr12:59989806-59990119	GM12891	blood:	n/a	n/a
18	CTCF	chr12:59989980-59990130	SK-N-SH_RA	brain:	n/a	n/a
19	TAF1	chr12:59989803-59990075	GM12878	blood:	n/a	n/a
20	MAZ	chr12:59989015-59992085	IMR90	lung:	n/a	chr12:59990810-59990825
21	CTCF	chr12:59989805-59990078	GM12878	blood:	n/a	n/a
22	POLR2A	chr12:59989257-59991805	GM12891	blood:	n/a	n/a
23	CTCF	chr12:59989920-59990070	HCPEpiC	choroid plexus:	n/a	n/a
24	MYC	chr12:59990047-59990447	MCF-7	breast:	n/a	n/a
25	MAX	chr12:59989500-59991421	GM12878	blood:	n/a	chr12:59990810-59990825
26	POLR2A	chr12:59989367-59991683	GM19193	blood:	n/a	n/a
27	MAX	chr12:59989757-59991112	H1-hESC	embryonic stem cell:	n/a	chr12:59990810-59990825
28	STAT1	chr12:59989489-59991608	Hela-S3	cervix:	n/a	chr12:59989845-59989857
29	POLR2A	chr12:59989730-59991574	GM12878	blood:	n/a	n/a
30	POLR2A	chr12:59989621-59990175	HUVEC	blood vessel:	n/a	n/a
31	POLR2A	chr12:59989458-59991600	Hela-S3	cervix:	n/a	n/a
32	CTCF	chr12:59989940-59990090	GM06990	blood:	n/a	n/a
33	E2F6	chr12:59989795-59990492	A549	lung:	n/a	chr12:59990273-59990282 chr12:59989851-59989863 chr12:59989841-59989850
34	POLR2A	chr12:59989339-59991769	MCF10A-Er-Src	breast:	n/a	n/a
35	POLR2A	chr12:59989934-59991033	GM12892	blood:	n/a	n/a
36	CREB1	chr12:59989775-59991005	H1-hESC	embryonic stem cell:	n/a	n/a
37	REST	chr12:59989759-59990203	PFSK-1	brain:	n/a	chr12:59990104-59990122 chr12:59990106-59990119 chr12:59990106-59990119
38	POLR2A	chr12:59989354-59991625	HL-60	blood:	n/a	n/a
39	MAX	chr12:59989820-59991020	MCF-7	breast:	n/a	chr12:59990810-59990825
40	POLR2A	chr12:59989388-59991638	GM18505	blood:	n/a	n/a
41	MAX	chr12:59989619-59991107	H1-hESC	embryonic stem cell:	n/a	chr12:59990810-59990825
42	POLR2A	chr12:59989356-59991738	HL-60	blood:	n/a	n/a
43	POLR2A	chr12:59989395-59991693	U87	brain:	n/a	n/a
44	POLR2A	chr12:59989653-59990380	HUVEC	blood vessel:	n/a	n/a
45	CTCF	chr12:59989920-59990070	NHDF-neo	bronchial:	n/a	n/a
46	TAF1	chr12:59989752-59990122	PFSK-1	brain:	n/a	n/a
47	MYC	chr12:59989422-59991686	MCF10A-Er-Src	breast:	n/a	chr12:59990810-59990825
48	ELK1	chr12:59989912-59990135	Hela-S3	cervix:	n/a	n/a
49	MXI1	chr12:59989471-59990195	H1-hESC	embryonic stem cell:	n/a	n/a
50	ARID3A	chr12:59990012-59990103	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:59989688..59990375-chr9:133568932..133569541,2	Hela-S3	cervix:
2	chr12:59989792..59990315-chr20:388080..388989,2	Hela-S3	cervix:

Variant related genes	Relation type
SLC16A7	TF binding region
ENSG00000125826	Chromatin interaction
ENSG00000130713	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs35285993	1.00[EUR][1000 genomes]
rs35831221	1.00[EUR][1000 genomes]
rs71463216	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7315997	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762982	chr12:59659871-60000135	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv1042271	chr12:59668468-59993468	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1038467	chr12:59680717-59999008	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv541507	chr12:59680717-59999008	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1049084	chr12:59700333-59993468	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv869425	chr12:59746898-60479741	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
7	nsv899131	chr12:59942122-60124089	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv1048949	chr12:59974039-60041477	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1038100	chr12:59983391-60018745	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59988800-59991000	Active TSS	Thymus	Thymus
2	chr12:59988800-59991600	Active TSS	Duodenum Mucosa	Duodenum
3	chr12:59988800-59991800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr12:59989000-59990400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr12:59989000-59990600	Active TSS	Primary T cells fromperipheralblood	blood
6	chr12:59989000-59990600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:59989000-59990600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr12:59989000-59990600	Active TSS	Fetal Brain Male	brain
9	chr12:59989000-59990600	Active TSS	Stomach Smooth Muscle	stomach
10	chr12:59989000-59990800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr12:59989000-59991000	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr12:59989000-59991000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr12:59989000-59991000	Active TSS	Fetal Brain Female	brain
14	chr12:59989000-59991000	Active TSS	Fetal Thymus	thymus
15	chr12:59989000-59991000	Active TSS	NHLF	lung
16	chr12:59989000-59991400	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr12:59989000-59991400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr12:59989000-59991400	Active TSS	Right Ventricle	heart
19	chr12:59989000-59991600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr12:59989000-59991600	Active TSS	Brain Germinal Matrix	brain
21	chr12:59989000-59991600	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr12:59989000-59992000	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr12:59989200-59990400	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr12:59989200-59990600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr12:59989200-59990600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr12:59989200-59990600	Active TSS	HSMM	muscle
27	chr12:59989200-59990800	Active TSS	Fetal Muscle Leg	muscle
28	chr12:59989200-59991000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr12:59989200-59991000	Active TSS	Primary B cells from peripheral blood	blood
30	chr12:59989200-59991000	Active TSS	Primary T killer memory cells from peripheral blood	blood
31	chr12:59989200-59991000	Active TSS	Brain Anterior Caudate	brain
32	chr12:59989200-59991000	Active TSS	Fetal Intestine Large	intestine
33	chr12:59989200-59991200	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr12:59989200-59991200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr12:59989200-59991200	Active TSS	Brain Angular Gyrus	brain
36	chr12:59989200-59991200	Active TSS	Brain Cingulate Gyrus	brain
37	chr12:59989200-59991200	Active TSS	Brain Substantia Nigra	brain
38	chr12:59989200-59991200	Active TSS	Colon Smooth Muscle	Colon
39	chr12:59989200-59991200	Active TSS	Hela-S3	cervix
40	chr12:59989200-59991200	Active TSS	HSMMtube	muscle
41	chr12:59989200-59991400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
42	chr12:59989200-59991400	Active TSS	Fetal Muscle Trunk	muscle
43	chr12:59989200-59991400	Active TSS	Psoas Muscle	Psoas
44	chr12:59989200-59991400	Bivalent/Poised TSS	A549	lung
45	chr12:59989200-59991600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr12:59989200-59991600	Active TSS	GM12878-XiMat	blood
47	chr12:59989200-59991800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr12:59989200-59991800	Active TSS	NHDF-Ad	bronchial
49	chr12:59989200-59992000	Active TSS	Aorta	Aorta
50	chr12:59989200-59992000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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