Variant report

Variant	rs17102066
Chromosome Location	chr1:46657799-46657800
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	chr1:46657772-46657907	K562	blood:	n/a	n/a
2	POLR2A	chr1:46657644-46657887	HCT-116	colon:	n/a	n/a
3	POLR2A	chr1:46657641-46658530	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr1:46657770-46658271	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr1:46657634-46664634	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:46641730..46644233-chr1:46656558..46658079,2	K562	blood:
2	chr1:46655107..46657515-chr1:46657628..46660092,2	K562	blood:

Variant related genes	Relation type
POMGNT1	TF binding region
ENSG00000250719	Chromatin interaction
ENSG00000117461	Chromatin interaction
ENSG00000085998	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs17102179	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2275425	1.00[AMR][1000 genomes]
rs28363193	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41378047	1.00[AMR][1000 genomes]
rs57121950	1.00[AMR][1000 genomes]
rs57959845	1.00[AMR][1000 genomes]
rs57991520	1.00[AMR][1000 genomes]
rs58888694	1.00[AMR][1000 genomes]
rs59006610	1.00[AMR][1000 genomes]
rs59669845	1.00[AMR][1000 genomes]
rs59768249	1.00[AMR][1000 genomes]
rs59919818	1.00[AMR][1000 genomes]
rs60411062	1.00[AMR][1000 genomes]
rs60789947	1.00[AMR][1000 genomes]
rs60933200	1.00[AMR][1000 genomes]
rs61178863	1.00[AMR][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	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
2	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
3	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
5	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
6	nsv527878	chr1:46649046-46660295	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv822520	chr1:46650486-46661701	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46645200-46657800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr1:46645600-46658200	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr1:46645800-46663200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:46648400-46657800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr1:46649400-46662400	Strong transcription	Fetal Stomach	stomach
6	chr1:46649800-46659800	Weak transcription	Fetal Heart	heart
7	chr1:46649800-46661400	Weak transcription	Psoas Muscle	Psoas
8	chr1:46649800-46663000	Weak transcription	HUVEC	blood vessel
9	chr1:46650400-46662600	Weak transcription	Right Atrium	heart
10	chr1:46650800-46662200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr1:46650800-46662600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr1:46651000-46662400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr1:46651000-46662600	Strong transcription	Fetal Muscle Leg	muscle
14	chr1:46651200-46662800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr1:46651200-46663000	Strong transcription	NHLF	lung
16	chr1:46651600-46662600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:46652000-46663200	Weak transcription	Fetal Kidney	kidney
18	chr1:46652600-46662800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:46652800-46658200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr1:46652800-46659800	Strong transcription	Colon Smooth Muscle	Colon
21	chr1:46652800-46660000	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr1:46652800-46660000	Strong transcription	Adipose Nuclei	Adipose
23	chr1:46652800-46660200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:46652800-46660400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr1:46652800-46660400	Strong transcription	Brain Germinal Matrix	brain
26	chr1:46652800-46660400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr1:46652800-46661600	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr1:46652800-46661800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr1:46652800-46662200	Strong transcription	Brain Cingulate Gyrus	brain
30	chr1:46652800-46662400	Strong transcription	Primary T cells from cord blood	blood
31	chr1:46652800-46662400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr1:46652800-46662400	Strong transcription	Fetal Muscle Trunk	muscle
33	chr1:46652800-46662800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:46652800-46662800	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr1:46653000-46658600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:46653000-46659600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr1:46653000-46659800	Strong transcription	Brain Anterior Caudate	brain
38	chr1:46653000-46660600	Strong transcription	Brain Hippocampus Middle	brain
39	chr1:46653000-46662200	Strong transcription	Brain Angular Gyrus	brain
40	chr1:46653000-46662200	Strong transcription	Dnd41	blood
41	chr1:46653000-46662400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:46653000-46662400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr1:46653000-46662400	Strong transcription	Fetal Brain Female	brain
44	chr1:46653000-46662400	Strong transcription	Stomach Smooth Muscle	stomach
45	chr1:46653000-46662600	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr1:46653000-46662600	Strong transcription	Thymus	Thymus
47	chr1:46653000-46662800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr1:46653200-46661800	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr1:46653200-46662200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr1:46653200-46662400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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