Variant report

Variant	rs2282227
Chromosome Location	chr1:154243097-154243098
allele	A/C/G/T
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:11)
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	POLR2A	chr1:154243096-154243547	K562	blood:	n/a	n/a
2	EP300	chr1:154243067-154243107	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:154242881-154245616	PFSK-1	brain:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:154241953..154243786-chr1:154320035..154322316,2	MCF-7	breast:
2	chr1:154186853..154188633-chr1:154242456..154244980,2	K562	blood:
3	chr1:154150174..154152704-chr1:154242243..154245750,3	MCF-7	breast:
4	chr1:154191842..154194909-chr1:154241050..154247826,7	K562	blood:
5	chr1:154241757..154243694-chr1:154292444..154293949,2	K562	blood:
6	chr1:154237893..154239947-chr1:154241262..154243106,2	K562	blood:
7	chr1:154191445..154194835-chr1:154242300..154245672,3	MCF-7	breast:
8	chr1:154233917..154236308-chr1:154240684..154243622,2	MCF-7	breast:
9	chr1:154229083..154233148-chr1:154241548..154245187,5	K562	blood:
10	chr1:154196130..154197678-chr1:154240668..154243583,2	K562	blood:
11	chr1:154242198..154244909-chr1:154262951..154265772,2	K562	blood:

No data

Variant related genes	Relation type
HAX1	TF binding region
ENSG00000143569	Chromatin interaction
ENSG00000143612	Chromatin interaction
ENSG00000143595	Chromatin interaction
ENSG00000201129	Chromatin interaction
ENSG00000143549	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10158820	0.84[ASN][1000 genomes]
rs1044013	0.86[ASN][1000 genomes]
rs1194593	0.87[ASN][1000 genomes]
rs1194596	0.87[ASN][1000 genomes]
rs12023901	0.94[ASN][1000 genomes]
rs12025237	0.96[ASN][1000 genomes]
rs12026615	0.96[ASN][1000 genomes]
rs12027999	0.95[ASN][1000 genomes]
rs12028554	0.82[ASN][1000 genomes]
rs12062977	0.84[ASN][1000 genomes]
rs12135346	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12733060	0.96[ASN][1000 genomes]
rs12738393	0.96[ASN][1000 genomes]
rs12742691	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12743874	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12749447	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12750321	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1760801	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1986709	0.82[ASN][1000 genomes]
rs2274993	0.96[ASN][1000 genomes]
rs2340473	0.84[ASN][1000 genomes]
rs2879788	0.82[ASN][1000 genomes]
rs3762339	0.84[ASN][1000 genomes]
rs3762340	0.92[ASN][1000 genomes]
rs3790613	0.96[ASN][1000 genomes]
rs3790614	0.96[ASN][1000 genomes]
rs3811453	0.88[ASN][1000 genomes]
rs3828077	0.96[ASN][1000 genomes]
rs4240871	0.82[ASN][1000 genomes]
rs6427509	0.84[ASN][1000 genomes]
rs6657214	0.82[ASN][1000 genomes]
rs6673752	0.96[ASN][1000 genomes]
rs6719	0.82[ASN][1000 genomes]
rs7517578	0.81[ASN][1000 genomes]
rs7522777	0.83[ASN][1000 genomes]
rs9943093	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
4	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
5	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
6	esv3451054	chr1:154182013-154360141	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 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	chr1:154195600-154244000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:154196200-154243800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr1:154196400-154243800	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr1:154196600-154243600	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr1:154197000-154243200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:154197000-154243600	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:154197000-154243800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr1:154197000-154243800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:154197200-154243600	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:154197200-154244000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:154197600-154243600	Strong transcription	H1 Cell Line	embryonic stem cell
12	chr1:154197600-154243600	Strong transcription	Muscle Satellite Cultured Cells	--
13	chr1:154197600-154243600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:154197600-154243600	Strong transcription	Thymus	Thymus
15	chr1:154197600-154243800	Strong transcription	Adipose Nuclei	Adipose
16	chr1:154197600-154244000	Strong transcription	Fetal Muscle Leg	muscle
17	chr1:154197800-154243600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:154197800-154243600	Strong transcription	Placenta	Placenta
19	chr1:154197800-154243800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:154198000-154243800	Strong transcription	Fetal Muscle Trunk	muscle
21	chr1:154199000-154243600	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr1:154199400-154243600	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr1:154200000-154243800	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr1:154211000-154243800	Strong transcription	Fetal Intestine Large	intestine
25	chr1:154213600-154243800	Strong transcription	Brain Hippocampus Middle	brain
26	chr1:154214000-154243600	Strong transcription	H9 Cell Line	embryonic stem cell
27	chr1:154214000-154243800	Strong transcription	Stomach Smooth Muscle	stomach
28	chr1:154219800-154244600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr1:154220000-154243200	Strong transcription	Lung	lung
30	chr1:154226400-154243600	Strong transcription	HSMM	muscle
31	chr1:154236600-154243800	Strong transcription	Osteobl	bone
32	chr1:154236800-154243600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:154236800-154243800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:154236800-154243800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr1:154236800-154244600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr1:154237000-154243800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:154237000-154244000	Weak transcription	Fetal Heart	heart
38	chr1:154237200-154243600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:154237200-154243800	Weak transcription	Hela-S3	cervix
40	chr1:154237600-154243400	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr1:154237800-154243800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:154237800-154243800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr1:154237800-154244000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr1:154238000-154243200	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr1:154238000-154243600	Strong transcription	Fetal Brain Female	brain
46	chr1:154238200-154243600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:154238400-154243200	Strong transcription	Fetal Intestine Small	intestine
48	chr1:154238400-154243600	Strong transcription	Fetal Stomach	stomach
49	chr1:154238400-154243800	Strong transcription	Placenta Amnion	Placenta Amnion
50	chr1:154238600-154243600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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