Variant report

Variant	rs2172708
Chromosome Location	chr1:154559795-154559796
allele	C/T
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	chr1:154554120-154560383	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:154557729..154560543-chr1:154574969..154576668,2	K562	blood:

Variant related genes	Relation type
ADAR	TF binding region
ENSG00000160710	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11264221	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11264231	0.81[YRI][hapmap];0.84[AFR][1000 genomes]
rs11264232	0.83[YRI][hapmap];0.84[AFR][1000 genomes]
rs11806816	0.81[YRI][hapmap];0.84[AFR][1000 genomes]
rs12079381	0.80[YRI][hapmap];0.84[AFR][1000 genomes]
rs12086987	0.85[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12094866	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1542796	0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6677920	0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6683149	0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6690277	0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7513474	0.85[AFR][1000 genomes]
rs9427095	0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][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	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
2	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
3	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
4	nsv427797	chr1:154559115-154933717	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154545400-154561800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:154547800-154578400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:154548000-154571800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:154548200-154575400	Strong transcription	Fetal Brain Female	brain
5	chr1:154548800-154575400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:154548800-154577400	Strong transcription	Fetal Intestine Small	intestine
7	chr1:154549200-154575800	Strong transcription	Brain Germinal Matrix	brain
8	chr1:154549400-154572200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:154549400-154575400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr1:154549400-154576200	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr1:154549400-154576200	Strong transcription	Primary T cells from cord blood	blood
12	chr1:154549400-154578000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr1:154549600-154572000	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr1:154549600-154575200	Strong transcription	Fetal Intestine Large	intestine
15	chr1:154549600-154576400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:154549800-154576400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr1:154549800-154576800	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr1:154550000-154570600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:154550000-154571000	Strong transcription	Brain Inferior Temporal Lobe	brain
20	chr1:154550000-154571400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:154550000-154574600	Strong transcription	A549	lung
22	chr1:154550200-154571800	Strong transcription	Fetal Thymus	thymus
23	chr1:154550200-154575200	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr1:154550200-154575200	Strong transcription	Placenta Amnion	Placenta Amnion
25	chr1:154550200-154576200	Strong transcription	Thymus	Thymus
26	chr1:154550200-154576400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr1:154550400-154566200	Strong transcription	Primary hematopoietic stem cells	blood
28	chr1:154550400-154566200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:154550400-154567800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:154550400-154571000	Strong transcription	Brain Hippocampus Middle	brain
31	chr1:154550400-154571400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:154550400-154571800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr1:154550400-154576200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
34	chr1:154550600-154564800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr1:154550600-154566000	Strong transcription	Gastric	stomach
36	chr1:154550600-154571200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:154550600-154571200	Strong transcription	Osteobl	bone
38	chr1:154550600-154571800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr1:154550600-154572000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr1:154550600-154572200	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr1:154550600-154572200	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr1:154550600-154575200	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr1:154550600-154576000	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr1:154550800-154566000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:154550800-154568000	Strong transcription	Muscle Satellite Cultured Cells	--
46	chr1:154550800-154568400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:154550800-154570800	Strong transcription	Brain Substantia Nigra	brain
48	chr1:154550800-154571000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr1:154550800-154571000	Strong transcription	Brain Cingulate Gyrus	brain
50	chr1:154550800-154571200	Strong transcription	NH-A	brain

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