Variant report

Variant	rs12090804
Chromosome Location	chr1:220146852-220146853
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr1:220146653-220147282	K562	blood:	n/a	n/a
2	GATA1	chr1:220146251-220146954	PBDE	blood:	n/a	n/a
3	POLR2A	chr1:220145349-220147798	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:220146511..220151613-chr1:220159074..220162362,5	K562	blood:
2	chr1:220146642..220149260-chr1:220156237..220158114,2	K562	blood:
3	chr1:220139066..220142338-chr1:220143870..220147751,4	K562	blood:
4	chr1:220144163..220148221-chr1:220163054..220166012,3	K562	blood:

No data

Variant related genes	Relation type
EPRS	TF binding region
ENSG00000136628	Chromatin interaction
ENSG00000238798	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11118481	1.00[AFR][1000 genomes]
rs11118482	1.00[AFR][1000 genomes]
rs12059273	0.91[AFR][1000 genomes]
rs12062082	1.00[AFR][1000 genomes]
rs12069364	0.91[AFR][1000 genomes]
rs12071410	1.00[AFR][1000 genomes]
rs12071984	0.91[AFR][1000 genomes]
rs12076227	1.00[AFR][1000 genomes]

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	nsv427930	chr1:220120379-220333434	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	744 gene(s)	inside rSNPs	diseases
2	nsv998124	chr1:220132739-220189211	Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	n/a
3	nsv832636	chr1:220139697-220294352	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	738 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220132800-220177000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:220139400-220154000	Weak transcription	Fetal Lung	lung
3	chr1:220140000-220167400	Weak transcription	Gastric	stomach
4	chr1:220140200-220151800	Weak transcription	NHLF	lung
5	chr1:220140200-220157600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:220140200-220160000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:220140400-220154200	Weak transcription	Esophagus	oesophagus
8	chr1:220140600-220162400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr1:220140600-220162400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:220140600-220163000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:220140800-220147000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:220140800-220150000	Strong transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:220140800-220150800	Strong transcription	Left Ventricle	heart
14	chr1:220140800-220161800	Strong transcription	Fetal Thymus	thymus
15	chr1:220140800-220162400	Strong transcription	Fetal Intestine Large	intestine
16	chr1:220140800-220162400	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr1:220140800-220163200	Strong transcription	Primary T cells from cord blood	blood
18	chr1:220140800-220164000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:220140800-220173400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:220140800-220192400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:220141000-220147200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:220141000-220149800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:220141000-220158000	Strong transcription	Primary B cells from peripheral blood	blood
24	chr1:220141000-220163000	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr1:220141000-220163200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:220141000-220163400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:220141200-220147000	Strong transcription	NH-A	brain
28	chr1:220141200-220152000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr1:220141200-220158200	Strong transcription	Rectal Mucosa Donor 29	rectum
30	chr1:220141200-220162000	Strong transcription	Adipose Nuclei	Adipose
31	chr1:220141200-220162800	Strong transcription	Duodenum Mucosa	Duodenum
32	chr1:220141200-220163200	Strong transcription	HSMM	muscle
33	chr1:220141200-220192200	Weak transcription	Fetal Kidney	kidney
34	chr1:220141400-220150000	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr1:220141400-220161800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:220141400-220162000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:220141400-220162200	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr1:220141400-220162200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr1:220141400-220163400	Strong transcription	Dnd41	blood
40	chr1:220141400-220165400	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr1:220141600-220147000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr1:220141600-220158000	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr1:220141600-220162000	Strong transcription	HUES48 Cell Line	embryonic stem cell
44	chr1:220141600-220162200	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr1:220141800-220157800	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr1:220142000-220147400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr1:220142000-220154600	Strong transcription	GM12878-XiMat	blood
48	chr1:220142200-220147000	Strong transcription	Primary B cells from cord blood	blood
49	chr1:220142200-220164000	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr1:220142400-220149600	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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