Variant report

Variant	rs28365208
Chromosome Location	chr12:40619826-40619827
allele	G/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	CHD1	chr12:40617719-40620681	GM12878	blood:	n/a	chr12:40618748-40618758
2	RCOR1	chr12:40619571-40620834	GM12878	blood:	n/a	n/a
3	EP300	chr12:40619754-40620414	GM12878	blood:	n/a	n/a
4	EBF1	chr12:40619613-40620945	GM12878	blood:	n/a	chr12:40620810-40620819
5	ZNF384	chr12:40619736-40620307	GM12878	blood:	n/a	n/a
6	POLR2A	chr12:40616826-40620140	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr12:40616780-40621231	GM18951	blood:	n/a	n/a
8	POLR2A	chr12:40617283-40620948	GM18526	blood:	n/a	n/a
9	TBP	chr12:40619440-40620658	GM12878	blood:	n/a	n/a
10	SPI1	chr12:40619630-40620808	GM12878	blood:	n/a	chr12:40620179-40620188
11	TBL1XR1	chr12:40619800-40620456	GM12878	blood:	n/a	n/a
12	EP300	chr12:40619571-40620612	GM12878	blood:	n/a	chr12:40620580-40620589
13	CEBPB	chr12:40619408-40619855	A549	lung:	n/a	chr12:40619599-40619608 chr12:40619597-40619610 chr12:40619598-40619609 chr12:40619599-40619608 chr12:40619599-40619608
14	CUX1	chr12:40619785-40620484	GM12878	blood:	n/a	n/a
15	POLR2A	chr12:40616564-40621335	GM19099	blood:	n/a	n/a
16	CEBPB	chr12:40619102-40619954	A549	lung:	n/a	chr12:40619599-40619608 chr12:40619597-40619610 chr12:40619598-40619609 chr12:40619599-40619608 chr12:40619599-40619608
17	NFIC	chr12:40619760-40620678	GM12878	blood:	n/a	n/a
18	FOS	chr12:40619517-40619835	MCF10A-Er-Src	breast:	n/a	n/a
19	MYC	chr12:40619543-40619881	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr12:40617353-40620863	GM15510	blood:	n/a	n/a
21	POLR2A	chr12:40618475-40620954	GM12878	blood:	n/a	n/a
22	POLR2A	chr12:40616903-40621176	GM19193	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:40615913..40618239-chr12:40619276..40621204,2	K562	blood:

Variant related genes	Relation type
ENSG00000225342	TF binding region
ENSG00000225342	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11564134	1.00[CEU][hapmap]
rs11564136	1.00[CEU][hapmap]
rs11564154	1.00[CEU][hapmap]
rs11564174	1.00[CEU][hapmap]
rs11564186	1.00[CEU][hapmap]
rs11564188	1.00[CEU][hapmap]
rs11564198	0.82[CHB][hapmap]
rs11564208	1.00[CEU][hapmap]
rs11564254	1.00[CEU][hapmap]
rs11564257	1.00[CEU][hapmap]
rs17442283	1.00[CHB][hapmap]
rs17443234	1.00[CHB][hapmap]
rs17443546	0.89[CHB][hapmap]
rs17444075	1.00[CHB][hapmap]
rs17458100	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17458452	1.00[CHB][hapmap]
rs17466009	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17466227	1.00[CHB][hapmap]
rs17466444	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17467046	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs17484093	0.91[CHB][hapmap]
rs17489542	1.00[CHB][hapmap]
rs17490692	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17490928	1.00[CHB][hapmap]
rs17492173	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17518134	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17519173	1.00[CEU][hapmap]
rs17519531	1.00[CEU][hapmap]
rs17519580	1.00[CEU][hapmap]
rs2254475	1.00[CEU][hapmap]
rs28365241	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs7315719	1.00[CEU][hapmap]
rs7315853	1.00[CEU][hapmap]
rs7316047	1.00[CEU][hapmap]
rs7974320	1.00[CEU][hapmap]

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	nsv1044685	chr12:40574460-40771612	Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1052661	chr12:40603049-40642812	Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40616000-40621200	Active TSS	Primary monocytes fromperipheralblood	blood
2	chr12:40616600-40621000	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr12:40616800-40620800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:40617000-40620600	Active TSS	Fetal Kidney	kidney
5	chr12:40617400-40620600	Active TSS	Stomach Smooth Muscle	stomach
6	chr12:40617400-40620800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:40617400-40620800	Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr12:40617400-40621000	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr12:40617400-40621000	Active TSS	Right Atrium	heart
10	chr12:40617400-40621400	Active TSS	Aorta	Aorta
11	chr12:40617600-40620200	Active TSS	Ovary	ovary
12	chr12:40617600-40620200	Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr12:40617600-40620800	Active TSS	Brain Anterior Caudate	brain
14	chr12:40617800-40620000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:40617800-40620400	Active TSS	Brain Angular Gyrus	brain
16	chr12:40617800-40620800	Active TSS	Brain Hippocampus Middle	brain
17	chr12:40617800-40621000	Active TSS	Rectal Smooth Muscle	rectum
18	chr12:40618000-40620400	Active TSS	Brain Substantia Nigra	brain
19	chr12:40618000-40620400	Active TSS	Psoas Muscle	Psoas
20	chr12:40618000-40620800	Active TSS	Lung	lung
21	chr12:40618000-40621000	Active TSS	A549	lung
22	chr12:40618200-40620000	Active TSS	Colon Smooth Muscle	Colon
23	chr12:40618200-40620600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
24	chr12:40618200-40620800	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr12:40618200-40620800	Active TSS	Rectal Mucosa Donor 31	rectum
26	chr12:40618800-40620800	Flanking Active TSS	GM12878-XiMat	blood
27	chr12:40618800-40621200	Flanking Active TSS	Primary B cells from cord blood	blood
28	chr12:40619000-40621000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr12:40619000-40621000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
30	chr12:40619200-40620200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr12:40619200-40620200	Flanking Active TSS	Adipose Nuclei	Adipose
32	chr12:40619200-40620200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr12:40619200-40621200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
34	chr12:40619400-40620000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr12:40619400-40620000	Flanking Active TSS	NHLF	lung
36	chr12:40619400-40620200	Active TSS	Placenta	Placenta
37	chr12:40619400-40620200	Weak transcription	NH-A	brain
38	chr12:40619400-40620400	Weak transcription	Hela-S3	cervix
39	chr12:40619400-40620800	Active TSS	Brain Cingulate Gyrus	brain
40	chr12:40619400-40620800	Active TSS	Duodenum Mucosa	Duodenum
41	chr12:40619400-40621000	Enhancers	HUVEC	blood vessel
42	chr12:40619400-40634600	Weak transcription	Spleen	Spleen
43	chr12:40619400-40644400	Weak transcription	Gastric	stomach
44	chr12:40619600-40620000	Active TSS	Primary hematopoietic stem cells	blood
45	chr12:40619600-40620000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr12:40619600-40620200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr12:40619600-40620600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr12:40619600-40620600	Weak transcription	Esophagus	oesophagus
49	chr12:40619600-40620600	Weak transcription	Left Ventricle	heart
50	chr12:40619600-40620600	Weak transcription	Pancreas	Pancrea

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