Variant report

Variant	rs12046966
Chromosome Location	chr1:78442764-78442765
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:78442194-78445438	GM12878	blood:	n/a	n/a
2	CHD1	chr1:78442498-78442914	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:78442372-78442821	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr1:78442414-78443002	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr1:78442194-78442835	GM12892	blood:	n/a	n/a
6	POLR2A	chr1:78442189-78442768	GM12892	blood:	n/a	n/a
7	WRNIP1	chr1:78442152-78443240	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:78442427-78445459	GM12878	blood:	n/a	n/a
9	POLR2A	chr1:78442143-78443347	SK-N-MC	brain:	n/a	n/a
10	POLR2A	chr1:78440937-78445383	K562	blood:	n/a	n/a
11	HEY1	chr1:78442313-78442781	K562	blood:	n/a	n/a
12	POLR2A	chr1:78442073-78442918	H1-hESC	embryonic stem cell:	n/a	n/a
13	MAX	chr1:78442461-78442787	NB4	blood:	n/a	n/a
14	POLR2A	chr1:78442521-78446101	PFSK-1	brain:	n/a	n/a
15	POLR2A	chr1:78442029-78445547	GM12878	blood:	n/a	n/a
16	POLR2A	chr1:78442152-78442803	GM12892	blood:	n/a	n/a
17	TCF7L2	chr1:78442521-78442878	Hela-S3	cervix:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:78419725..78422750-chr1:78442650..78445885,3	MCF-7	breast:
2	chr1:78441900..78447727-chr1:78466477..78473207,15	MCF-7	breast:
3	chr1:78441362..78443969-chr1:78545013..78547502,2	K562	blood:
4	chr1:78442485..78444153-chr8:102209563..102211525,2	MCF-7	breast:
5	chr1:78441980..78446801-chr1:78467462..78471771,12	MCF-7	breast:

No data

Variant related genes	Relation type
DNAJB4	TF binding region
GIPC2	TF binding region
ENSG00000273338	Chromatin interaction
ENSG00000162613	Chromatin interaction
ENSG00000162616	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10518561	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs12027183	1.00[CEU][hapmap]
rs12027558	1.00[CEU][hapmap]
rs12035132	1.00[CEU][hapmap]
rs7528905	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[CHD][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap]

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	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv518855	chr1:78416669-78456355	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78432600-78443400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:78433800-78443600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:78439400-78442800	Genic enhancers	Primary B cells from peripheral blood	blood
4	chr1:78440200-78443600	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
5	chr1:78440200-78444000	Transcr. at gene 5' and 3'	Dnd41	blood
6	chr1:78440200-78444400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
7	chr1:78440200-78445200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
8	chr1:78440600-78442800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:78440600-78442800	Transcr. at gene 5' and 3'	K562	blood
10	chr1:78440800-78442800	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
11	chr1:78440800-78442800	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
12	chr1:78440800-78442800	Transcr. at gene 5' and 3'	Osteobl	bone
13	chr1:78440800-78443000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:78440800-78443000	Transcr. at gene 5' and 3'	HSMM	muscle
15	chr1:78440800-78444400	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
16	chr1:78441200-78442800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:78441200-78443000	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:78441200-78443000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr1:78441200-78443000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:78441200-78443000	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr1:78441200-78443000	Flanking Active TSS	HUVEC	blood vessel
22	chr1:78441200-78443200	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr1:78441200-78443400	Flanking Active TSS	Fetal Brain Male	brain
24	chr1:78441200-78443600	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr1:78441200-78443800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr1:78441200-78444600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:78441200-78446200	Active TSS	Aorta	Aorta
28	chr1:78441400-78443000	Flanking Active TSS	Brain Hippocampus Middle	brain
29	chr1:78441400-78443200	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr1:78441400-78443600	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 2	blood
31	chr1:78441400-78444000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
32	chr1:78441400-78444000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:78441400-78446800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:78441600-78442800	Flanking Active TSS	Brain Anterior Caudate	brain
35	chr1:78441600-78442800	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
36	chr1:78441600-78443000	Flanking Active TSS	Brain Substantia Nigra	brain
37	chr1:78441600-78443000	Flanking Active TSS	Fetal Brain Female	brain
38	chr1:78441600-78443000	Transcr. at gene 5' and 3'	Fetal Lung	lung
39	chr1:78441600-78446000	Active TSS	Colonic Mucosa	Colon
40	chr1:78441800-78443000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
41	chr1:78441800-78443000	Transcr. at gene 5' and 3'	NHEK	skin
42	chr1:78441800-78445600	Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr1:78441800-78446200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr1:78442000-78442800	Enhancers	Primary B cells from cord blood	blood
45	chr1:78442000-78443000	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:78442000-78443200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
47	chr1:78442000-78446200	Active TSS	Brain Angular Gyrus	brain
48	chr1:78442000-78446800	Active TSS	GM12878-XiMat	blood
49	chr1:78442000-78447200	Active TSS	A549	lung
50	chr1:78442200-78442800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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