Variant report

Variant	rs2968790
Chromosome Location	chr2:55280594-55280595
allele	C/G
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	FOSL1	chr2:55280471-55280663	K562	blood:	n/a	n/a
2	JUND	chr2:55280348-55280973	K562	blood:	n/a	n/a
3	CUX1	chr2:55280439-55280609	K562	blood:	n/a	n/a
4	JUN	chr2:55279957-55280704	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:

Variant related genes	Relation type
RTN4	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10174838	0.84[EUR][1000 genomes]
rs10210840	0.82[EUR][1000 genomes]
rs11674808	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12713284	0.86[EUR][1000 genomes]
rs13011689	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13387751	0.84[EUR][1000 genomes]
rs2044291	0.84[EUR][1000 genomes]
rs2580772	0.82[EUR][1000 genomes]
rs2580776	0.82[EUR][1000 genomes]
rs2860453	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2919129	0.82[EUR][1000 genomes]
rs2920862	0.81[ASN][1000 genomes]
rs2920878	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2920893	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2920900	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2968786	0.86[EUR][1000 genomes]
rs2968793	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2968794	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2968795	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2968798	0.81[ASN][1000 genomes]
rs2968822	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2968825	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2968827	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2972070	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2972071	0.85[ASN][1000 genomes]
rs2972072	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2972075	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2972097	0.87[EUR][1000 genomes]
rs35631428	0.83[EUR][1000 genomes]
rs4672005	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6545466	0.86[EUR][1000 genomes]
rs6726158	0.84[EUR][1000 genomes]
rs6755468	0.84[EUR][1000 genomes]
rs6760429	0.86[EUR][1000 genomes]
rs7340476	0.84[EUR][1000 genomes]
rs7562292	0.86[EUR][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

No data

Chromatin state (count:61 , 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	chr2:55278800-55280600	Active TSS	K562	blood
7	chr2:55278800-55282200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr2:55278800-55283200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr2:55278800-55283200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr2:55278800-55288600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:55278800-55290800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr2:55279000-55282000	Enhancers	Primary B cells from peripheral blood	blood
13	chr2:55279000-55282400	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr2:55279000-55283200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr2:55279000-55287000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr2:55279000-55290600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr2:55279400-55281000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr2:55279400-55281000	Weak transcription	Thymus	Thymus
19	chr2:55279400-55282000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr2:55279400-55282200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr2:55279400-55283000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:55279400-55283200	Weak transcription	Osteobl	bone
23	chr2:55279400-55283400	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr2:55279400-55283400	Weak transcription	Brain Hippocampus Middle	brain
25	chr2:55279400-55287600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr2:55279600-55281400	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr2:55279600-55281400	Weak transcription	Fetal Kidney	kidney
28	chr2:55279600-55283000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:55279600-55283200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr2:55279800-55280800	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr2:55279800-55280800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr2:55279800-55280800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:55279800-55281400	Enhancers	Primary T cells from cord blood	blood
34	chr2:55279800-55282000	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr2:55279800-55282000	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr2:55279800-55282600	Enhancers	Primary B cells from cord blood	blood
37	chr2:55279800-55283200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr2:55279800-55283200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:55279800-55283200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr2:55279800-55283200	Weak transcription	NHDF-Ad	bronchial
41	chr2:55279800-55284200	Weak transcription	Fetal Intestine Small	intestine
42	chr2:55279800-55284400	Weak transcription	Fetal Heart	heart
43	chr2:55279800-55287400	Weak transcription	HSMM	muscle
44	chr2:55280000-55280800	Enhancers	GM12878-XiMat	blood
45	chr2:55280000-55281000	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr2:55280000-55281200	Enhancers	Primary hematopoietic stem cells	blood
47	chr2:55280000-55281600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr2:55280000-55281800	Enhancers	Dnd41	blood
49	chr2:55280000-55282800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr2:55280000-55283000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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