Variant report

Variant	rs17046564
Chromosome Location	chr2:55217134-55217135
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	chr2:55212432-55217795	K562	blood:	n/a	n/a
2	POLR2A	chr2:55216899-55217156	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:55216168..55220754-chr2:55221880..55224884,4	MCF-7	breast:
2	chr2:55215896..55218354-chr2:55222752..55225132,2	K562	blood:
3	chr2:55215664..55218100-chr2:55259563..55261709,2	K562	blood:

Variant related genes	Relation type
RTN4	TF binding region

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11884082	1.00[AMR][1000 genomes]
rs11892015	1.00[AMR][1000 genomes]
rs11895689	0.85[AMR][1000 genomes]
rs11899197	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11899295	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs15028	1.00[AMR][1000 genomes]
rs17046545	1.00[AMR][1000 genomes]
rs2864047	0.85[AMR][1000 genomes]
rs2864048	0.85[AMR][1000 genomes]
rs55697927	0.98[AFR][1000 genomes]
rs55879444	0.98[AFR][1000 genomes]
rs56290934	0.98[AFR][1000 genomes]
rs58156158	1.00[AMR][1000 genomes]
rs58482670	0.96[AFR][1000 genomes]
rs73936506	0.85[AMR][1000 genomes]
rs73936508	0.85[AMR][1000 genomes]
rs73936512	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73936517	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73936518	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73936805	0.92[AFR][1000 genomes]
rs73936812	0.96[AFR][1000 genomes]
rs73936813	0.96[AFR][1000 genomes]
rs73936821	1.00[AMR][1000 genomes]
rs73936824	1.00[AMR][1000 genomes]
rs957920	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834069	chr2:55096597-55251680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv874155	chr2:55205262-55307646	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55191800-55234200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:55196200-55226400	Weak transcription	Thymus	Thymus
3	chr2:55196600-55217200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:55196600-55217200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:55198200-55237200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:55203800-55222600	Weak transcription	Spleen	Spleen
7	chr2:55203800-55223800	Weak transcription	Pancreas	Pancrea
8	chr2:55203800-55258400	Weak transcription	Esophagus	oesophagus
9	chr2:55205200-55220600	Weak transcription	Small Intestine	intestine
10	chr2:55205200-55223800	Weak transcription	Left Ventricle	heart
11	chr2:55210000-55228200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr2:55211000-55218600	Weak transcription	Aorta	Aorta
13	chr2:55211200-55232000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:55212200-55220600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr2:55212600-55220200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr2:55212600-55226400	Weak transcription	Fetal Stomach	stomach
17	chr2:55213200-55217200	Strong transcription	HSMM	muscle
18	chr2:55213400-55217200	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr2:55213800-55217200	Enhancers	Brain Substantia Nigra	brain
20	chr2:55213800-55226400	Weak transcription	Ovary	ovary
21	chr2:55214000-55218600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr2:55214200-55224600	Weak transcription	Primary T cells from cord blood	blood
23	chr2:55214200-55225000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr2:55214200-55234400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr2:55214400-55222800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr2:55214400-55232800	Weak transcription	Fetal Brain Female	brain
27	chr2:55214600-55225600	Weak transcription	NH-A	brain
28	chr2:55214600-55226000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr2:55214800-55217200	Enhancers	Brain Anterior Caudate	brain
30	chr2:55214800-55217400	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr2:55214800-55217600	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr2:55214800-55218000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr2:55214800-55218600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:55214800-55218600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:55214800-55218600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr2:55214800-55218600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr2:55214800-55218600	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr2:55214800-55219000	Weak transcription	NHEK	skin
39	chr2:55214800-55219200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr2:55214800-55219200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr2:55214800-55220600	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr2:55214800-55221600	Weak transcription	HSMMtube	muscle
43	chr2:55214800-55221800	Weak transcription	Primary B cells from peripheral blood	blood
44	chr2:55214800-55222000	Weak transcription	GM12878-XiMat	blood
45	chr2:55214800-55223600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr2:55214800-55223800	Weak transcription	Gastric	stomach
47	chr2:55214800-55224400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr2:55214800-55224400	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr2:55214800-55224600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr2:55214800-55225000	Weak transcription	Primary monocytes fromperipheralblood	blood

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