Variant report

Variant	rs7559248
Chromosome Location	chr2:55280967-55280968
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	JUND	chr2:55280348-55280973	K562	blood:	n/a	n/a
2	POLR2A	chr2:55280929-55281101	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:55278606..55281085-chr2:55289009..55290511,2	K562	blood:
2	chr2:55279956..55282350-chr2:55389384..55392221,3	K562	blood:
3	chr2:55278300..55281080-chr2:55325086..55327233,3	K562	blood:
4	chr2:55280650..55283253-chr2:55298459..55300307,2	K562	blood:

Variant related genes	Relation type
RTN4	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10179594	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10205017	0.88[EUR][1000 genomes]
rs12989576	0.90[EUR][1000 genomes]
rs13002841	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs13023202	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs13026576	1.00[AFR][1000 genomes]
rs17418111	1.00[AFR][1000 genomes]
rs2580763	0.85[EUR][1000 genomes]
rs2580766	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2588520	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2919125	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2920839	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920861	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2920863	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2920881	0.81[ASN][1000 genomes]
rs2920883	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2920884	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2920889	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2920890	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2920897	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2968789	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2968792	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2968823	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2968824	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2968826	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2968829	0.84[ASN][1000 genomes]
rs2968831	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2972065	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2972066	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2972067	0.81[ASN][1000 genomes]
rs2972069	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2972073	0.81[ASN][1000 genomes]
rs2972076	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3099068	0.81[ASN][1000 genomes]
rs34227740	1.00[AFR][1000 genomes]
rs34564860	1.00[AFR][1000 genomes]
rs36024305	1.00[AFR][1000 genomes]
rs4671233	1.00[AFR][1000 genomes]
rs55777421	1.00[AFR][1000 genomes]
rs67721747	1.00[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7559248	RTN4	cis	Thyroid	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55278200-55282600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:55278200-55288800	Weak transcription	Lung	lung
3	chr2:55278600-55281000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr2:55278600-55281600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr2:55278600-55282000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr2:55278800-55282200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:55278800-55283200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr2:55278800-55283200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr2:55278800-55288600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:55278800-55290800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:55279000-55282000	Enhancers	Primary B cells from peripheral blood	blood
12	chr2:55279000-55282400	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr2:55279000-55283200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr2:55279000-55287000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr2:55279000-55290600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr2:55279400-55281000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr2:55279400-55281000	Weak transcription	Thymus	Thymus
18	chr2:55279400-55282000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr2:55279400-55282200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr2:55279400-55283000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr2:55279400-55283200	Weak transcription	Osteobl	bone
22	chr2:55279400-55283400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr2:55279400-55283400	Weak transcription	Brain Hippocampus Middle	brain
24	chr2:55279400-55287600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr2:55279600-55281400	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr2:55279600-55281400	Weak transcription	Fetal Kidney	kidney
27	chr2:55279600-55283000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:55279600-55283200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr2:55279800-55281400	Enhancers	Primary T cells from cord blood	blood
30	chr2:55279800-55282000	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr2:55279800-55282000	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr2:55279800-55282600	Enhancers	Primary B cells from cord blood	blood
33	chr2:55279800-55283200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr2:55279800-55283200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:55279800-55283200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr2:55279800-55283200	Weak transcription	NHDF-Ad	bronchial
37	chr2:55279800-55284200	Weak transcription	Fetal Intestine Small	intestine
38	chr2:55279800-55284400	Weak transcription	Fetal Heart	heart
39	chr2:55279800-55287400	Weak transcription	HSMM	muscle
40	chr2:55280000-55281000	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr2:55280000-55281200	Enhancers	Primary hematopoietic stem cells	blood
42	chr2:55280000-55281600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr2:55280000-55281800	Enhancers	Dnd41	blood
44	chr2:55280000-55282800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr2:55280000-55283000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr2:55280000-55283200	Weak transcription	HMEC	breast
47	chr2:55280000-55289000	Weak transcription	HepG2	liver
48	chr2:55280200-55281400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr2:55280200-55281800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:55280200-55283200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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