Variant report

Variant	rs73936517
Chromosome Location	chr2:55216090-55216091
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	chr2:55215658-55216225	U87	brain:	n/a	n/a
3	POLR2A	chr2:55215917-55217097	A549	lung:	n/a	n/a
4	POLR2A	chr2:55215854-55216822	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr2:55215664-55216219	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55215896..55218354-chr2:55222752..55225132,2	K562	blood:
2	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	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11895689	0.85[AMR][1000 genomes]
rs11899197	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11899295	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs15028	1.00[AMR][1000 genomes]
rs17046545	1.00[AMR][1000 genomes]
rs17046564	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2864047	0.85[AMR][1000 genomes]
rs2864048	0.85[AMR][1000 genomes]
rs55697927	1.00[AFR][1000 genomes]
rs55879444	1.00[AFR][1000 genomes]
rs56290934	1.00[AFR][1000 genomes]
rs58156158	1.00[AMR][1000 genomes]
rs58482670	0.98[AFR][1000 genomes]
rs73936506	0.85[AMR][1000 genomes]
rs73936508	0.85[AMR][1000 genomes]
rs73936512	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73936518	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73936805	0.94[AFR][1000 genomes]
rs73936812	0.98[AFR][1000 genomes]
rs73936813	0.98[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:119 , 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	chr2:55195800-55216200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr2:55196200-55226400	Weak transcription	Thymus	Thymus
4	chr2:55196600-55217200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:55196600-55217200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr2:55198200-55237200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:55200800-55216600	Weak transcription	Colonic Mucosa	Colon
8	chr2:55203800-55222600	Weak transcription	Spleen	Spleen
9	chr2:55203800-55223800	Weak transcription	Pancreas	Pancrea
10	chr2:55203800-55258400	Weak transcription	Esophagus	oesophagus
11	chr2:55205200-55220600	Weak transcription	Small Intestine	intestine
12	chr2:55205200-55223800	Weak transcription	Left Ventricle	heart
13	chr2:55208200-55216600	Weak transcription	Stomach Mucosa	stomach
14	chr2:55210000-55228200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr2:55211000-55218600	Weak transcription	Aorta	Aorta
16	chr2:55211200-55232000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr2:55212200-55220600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr2:55212600-55220200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr2:55212600-55226400	Weak transcription	Fetal Stomach	stomach
20	chr2:55213200-55217200	Strong transcription	HSMM	muscle
21	chr2:55213400-55217200	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr2:55213800-55217200	Enhancers	Brain Substantia Nigra	brain
23	chr2:55213800-55226400	Weak transcription	Ovary	ovary
24	chr2:55214000-55216600	Weak transcription	Fetal Lung	lung
25	chr2:55214000-55218600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr2:55214200-55224600	Weak transcription	Primary T cells from cord blood	blood
27	chr2:55214200-55225000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr2:55214200-55234400	Weak transcription	Fetal Muscle Trunk	muscle
29	chr2:55214400-55222800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:55214400-55232800	Weak transcription	Fetal Brain Female	brain
31	chr2:55214600-55225600	Weak transcription	NH-A	brain
32	chr2:55214600-55226000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr2:55214800-55216200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr2:55214800-55216200	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr2:55214800-55216200	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr2:55214800-55216200	Weak transcription	NHDF-Ad	bronchial
37	chr2:55214800-55216600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:55214800-55216800	Weak transcription	Placenta	Placenta
39	chr2:55214800-55217000	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr2:55214800-55217000	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr2:55214800-55217000	Enhancers	Brain Hippocampus Middle	brain
42	chr2:55214800-55217200	Enhancers	Brain Anterior Caudate	brain
43	chr2:55214800-55217400	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr2:55214800-55217600	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr2:55214800-55218000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr2:55214800-55218600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr2:55214800-55218600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:55214800-55218600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr2:55214800-55218600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr2:55214800-55218600	Weak transcription	Muscle Satellite Cultured Cells	--

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