Variant report

Variant	rs3789457
Chromosome Location	chr1:94343233-94343234
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:94341699-94343563	K562	blood:	n/a	n/a
2	SPI1	chr1:94343149-94343387	K562	blood:	n/a	n/a
3	SPI1	chr1:94343163-94343509	HL-60	blood:	n/a	n/a
4	POLR2A	chr1:94342809-94343249	A549	lung:	n/a	n/a
5	POLR2A	chr1:94343044-94343327	GM12878	blood:	n/a	n/a
6	SPI1	chr1:94343050-94343486	HL-60	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:94336837..94340766-chr1:94341847..94346212,6	K562	blood:
2	chr1:94332079..94335914-chr1:94341026..94344306,4	K562	blood:
3	chr1:94343199..94347658-chr1:94372955..94376562,9	MCF-7	breast:
4	chr1:94311992..94315197-chr1:94341852..94346150,3	MCF-7	breast:
5	chr1:94312180..94314378-chr1:94343204..94344804,3	K562	blood:
6	chr1:94340990..94343514-chr1:94369991..94373741,3	K562	blood:
7	chr1:94342014..94348814-chr1:94369991..94376733,14	K562	blood:
8	chr1:94310214..94315053-chr1:94342432..94346579,12	K562	blood:

No data

Variant related genes	Relation type
DNTTIP2	TF binding region
ENSG00000023909	Chromatin interaction
ENSG00000260464	Chromatin interaction
ENSG00000211575	Chromatin interaction
ENSG00000067334	Chromatin interaction
ENSG00000137936	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1473712	0.83[EUR][1000 genomes]
rs1473713	0.94[EUR][1000 genomes]
rs1884019	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2064765	0.89[EUR][1000 genomes]
rs2143991	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2235970	0.84[JPT][hapmap]
rs2301022	0.88[CEU][hapmap];0.94[JPT][hapmap]
rs2747042	1.00[JPT][hapmap]
rs3789453	0.87[CEU][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap]
rs4847192	0.88[ASN][1000 genomes]
rs4847268	0.89[EUR][1000 genomes]
rs6660210	1.00[JPT][hapmap]
rs6683813	0.82[EUR][1000 genomes]
rs743110	0.96[CEU][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs743112	0.82[EUR][1000 genomes]
rs7523787	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7526082	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7526920	0.82[EUR][1000 genomes]
rs7552293	1.00[JPT][hapmap]
rs9725707	0.80[EUR][1000 genomes]
rs990576	0.90[EUR][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3789457	GCLM	cis	parietal	SCAN
rs3789457	GEMIN8P4	cis	cerebellum	SCAN
rs3789457	ALG14	cis	cerebellum	SCAN
rs3789457	GCLM	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94322200-94343600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:94329800-94343600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:94330600-94343600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:94334000-94343400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr1:94334200-94343400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
6	chr1:94334200-94343400	Strong transcription	Placenta	Placenta
7	chr1:94334400-94343400	Weak transcription	Fetal Heart	heart
8	chr1:94334600-94343400	Strong transcription	Fetal Muscle Trunk	muscle
9	chr1:94338400-94343800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr1:94340400-94343800	Weak transcription	Aorta	Aorta
11	chr1:94340400-94344000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:94340600-94343600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:94340600-94343600	Weak transcription	Lung	lung
14	chr1:94340600-94344000	Weak transcription	Esophagus	oesophagus
15	chr1:94340600-94344000	Weak transcription	Ovary	ovary
16	chr1:94341000-94343400	Weak transcription	Fetal Stomach	stomach
17	chr1:94341000-94343400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr1:94341200-94343400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:94341200-94343400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
20	chr1:94341600-94343400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:94341600-94343400	Genic enhancers	Primary B cells from cord blood	blood
22	chr1:94341600-94343400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr1:94341600-94343400	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr1:94341600-94343600	Genic enhancers	Primary hematopoietic stem cells	blood
25	chr1:94341600-94343600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr1:94341600-94343600	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr1:94341600-94343600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:94341600-94343600	Genic enhancers	Adipose Nuclei	Adipose
29	chr1:94341600-94343600	Genic enhancers	Liver	Liver
30	chr1:94341600-94343600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
31	chr1:94341600-94343600	Genic enhancers	Thymus	Thymus
32	chr1:94341600-94343600	Genic enhancers	HUVEC	blood vessel
33	chr1:94341600-94343600	Transcr. at gene 5' and 3'	K562	blood
34	chr1:94341600-94343800	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
35	chr1:94341800-94343400	Genic enhancers	Brain Angular Gyrus	brain
36	chr1:94341800-94343400	Genic enhancers	Duodenum Smooth Muscle	Duodenum
37	chr1:94341800-94343600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:94341800-94343600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
39	chr1:94341800-94343600	Genic enhancers	Brain Germinal Matrix	brain
40	chr1:94341800-94343600	Genic enhancers	Rectal Mucosa Donor 29	rectum
41	chr1:94341800-94343600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
42	chr1:94341800-94343600	Genic enhancers	Monocytes-CD14+_RO01746	blood
43	chr1:94341800-94344600	Transcr. at gene 5' and 3'	Dnd41	blood
44	chr1:94342000-94343400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:94342000-94343400	Genic enhancers	Fetal Brain Female	brain
46	chr1:94342000-94343400	Genic enhancers	Sigmoid Colon	Sigmoid Colon
47	chr1:94342000-94343400	Genic enhancers	Osteobl	bone
48	chr1:94342000-94343600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr1:94342000-94343600	Enhancers	Fetal Intestine Small	intestine
50	chr1:94342000-94343600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood

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