Variant report

Variant	rs1488085
Chromosome Location	chr1:154242349-154242350
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:154242349-154242374	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:154242050-154242822	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr1:154241873-154242373	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr1:154241903-154242350	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr1:154241539-154242671	K562	blood:	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	chr1:154150174..154152704-chr1:154242243..154245750,3	MCF-7	breast:
3	chr1:154191842..154194909-chr1:154241050..154247826,7	K562	blood:
4	chr1:154241102..154242733-chr1:154243304..154244878,2	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
ENSG00000143612	Chromatin interaction
ENSG00000143595	Chromatin interaction
ENSG00000143549	Chromatin interaction
ENSG00000143569	Chromatin interaction
ENSG00000201129	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12090237	1.00[CEU][hapmap]
rs16835819	1.00[AFR][1000 genomes]
rs16835877	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs34806329	1.00[AFR][1000 genomes]
rs72696231	1.00[AFR][1000 genomes]
rs72696240	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72696254	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72696264	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7411976	1.00[CEU][hapmap]

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	chr1:154196800-154242600	Strong transcription	A549	lung
6	chr1:154197000-154242800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr1:154197000-154243200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:154197000-154243600	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:154197000-154243800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr1:154197000-154243800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:154197200-154243600	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr1:154197200-154244000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:154197400-154242800	Strong transcription	Brain Anterior Caudate	brain
14	chr1:154197600-154243000	Strong transcription	Primary B cells from peripheral blood	blood
15	chr1:154197600-154243600	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr1:154197600-154243600	Strong transcription	Muscle Satellite Cultured Cells	--
17	chr1:154197600-154243600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:154197600-154243600	Strong transcription	Thymus	Thymus
19	chr1:154197600-154243800	Strong transcription	Adipose Nuclei	Adipose
20	chr1:154197600-154244000	Strong transcription	Fetal Muscle Leg	muscle
21	chr1:154197800-154243600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:154197800-154243600	Strong transcription	Placenta	Placenta
23	chr1:154197800-154243800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:154198000-154243000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:154198000-154243800	Strong transcription	Fetal Muscle Trunk	muscle
26	chr1:154198400-154243000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:154199000-154243600	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr1:154199400-154243600	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr1:154200000-154243800	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr1:154211000-154243800	Strong transcription	Fetal Intestine Large	intestine
31	chr1:154213000-154242800	Strong transcription	Colon Smooth Muscle	Colon
32	chr1:154213600-154243800	Strong transcription	Brain Hippocampus Middle	brain
33	chr1:154214000-154243600	Strong transcription	H9 Cell Line	embryonic stem cell
34	chr1:154214000-154243800	Strong transcription	Stomach Smooth Muscle	stomach
35	chr1:154214200-154242800	Strong transcription	NHEK	skin
36	chr1:154219800-154244600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr1:154220000-154243200	Strong transcription	Lung	lung
38	chr1:154225600-154242600	Strong transcription	Primary B cells from cord blood	blood
39	chr1:154226200-154242600	Strong transcription	Fetal Kidney	kidney
40	chr1:154226400-154243600	Strong transcription	HSMM	muscle
41	chr1:154236600-154243800	Strong transcription	Osteobl	bone
42	chr1:154236800-154243600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:154236800-154243800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr1:154236800-154243800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr1:154236800-154244600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr1:154237000-154243800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:154237000-154244000	Weak transcription	Fetal Heart	heart
48	chr1:154237200-154243600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:154237200-154243800	Weak transcription	Hela-S3	cervix
50	chr1:154237600-154243400	Strong transcription	Primary monocytes fromperipheralblood	blood

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