Variant report

Variant	rs12647779
Chromosome Location	chr4:106099311-106099312
allele	A/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	chr4:106098697-106099431	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:106064646..106070521-chr4:106098298..106104512,9	MCF-7	breast:

Variant related genes	Relation type
TET2-AS1	TF binding region
ENSG00000168769	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1114718	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11933960	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12498609	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12506006	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12511800	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12640842	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12642165	1.00[JPT][hapmap]
rs12647884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1391442	1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17583579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17583593	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17616993	0.88[EUR][1000 genomes]
rs2023841	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2088484	1.00[JPT][hapmap]
rs2866774	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6533180	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73836040	0.81[AFR][1000 genomes]
rs949681	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9637601	1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461609	chr4:105869548-106366209	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv470063	chr4:105869548-106366209	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv595007	chr4:105869548-106366209	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv830025	chr4:105988876-106137946	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106069400-106114200	Weak transcription	Esophagus	oesophagus
2	chr4:106069600-106102400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr4:106069800-106101000	Weak transcription	HSMM	muscle
4	chr4:106069800-106101800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr4:106070400-106107800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr4:106070400-106111600	Weak transcription	Placenta	Placenta
7	chr4:106071000-106100800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr4:106072600-106100600	Weak transcription	Adipose Nuclei	Adipose
9	chr4:106077000-106100800	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr4:106077000-106112000	Weak transcription	Aorta	Aorta
11	chr4:106078000-106112800	Weak transcription	Fetal Kidney	kidney
12	chr4:106080600-106101800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:106080600-106102800	Weak transcription	NHEK	skin
14	chr4:106080600-106105800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr4:106080600-106107800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr4:106083600-106100800	Weak transcription	Duodenum Mucosa	Duodenum
17	chr4:106083600-106100800	Weak transcription	Right Ventricle	heart
18	chr4:106083600-106109200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr4:106083800-106100400	Weak transcription	Stomach Mucosa	stomach
20	chr4:106083800-106104800	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr4:106083800-106111400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr4:106084000-106105000	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr4:106084800-106127400	Weak transcription	Brain Germinal Matrix	brain
24	chr4:106085600-106112800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr4:106086000-106105600	Weak transcription	Fetal Lung	lung
26	chr4:106089600-106100800	Weak transcription	Small Intestine	intestine
27	chr4:106090400-106105600	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr4:106090600-106107000	Weak transcription	NH-A	brain
29	chr4:106091400-106100600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr4:106091600-106100800	Weak transcription	Ovary	ovary
31	chr4:106092000-106105800	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr4:106092000-106110600	Weak transcription	Primary B cells from peripheral blood	blood
33	chr4:106093800-106100800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr4:106093800-106111200	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr4:106093800-106112400	Weak transcription	Primary B cells from cord blood	blood
36	chr4:106094000-106112600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr4:106094400-106102200	Weak transcription	Primary T cells from cord blood	blood
38	chr4:106095400-106101000	Weak transcription	HSMMtube	muscle
39	chr4:106096200-106100600	Weak transcription	HepG2	liver
40	chr4:106096200-106111600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr4:106096400-106100400	Weak transcription	Liver	Liver
42	chr4:106096400-106111200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr4:106096600-106107200	Weak transcription	Psoas Muscle	Psoas
44	chr4:106097400-106105800	Weak transcription	Primary hematopoietic stem cells	blood
45	chr4:106097600-106105600	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr4:106098000-106111400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr4:106098200-106102200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr4:106098200-106103400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr4:106098200-106113200	Weak transcription	Fetal Stomach	stomach
50	chr4:106098400-106102600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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