Variant report

Variant	rs7601895
Chromosome Location	chr2:55281901-55281902
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	EBF1	chr2:55281650-55282067	GM12878	blood:	n/a	n/a
2	PAX5	chr2:55281601-55281978	GM12891	blood:	n/a	n/a
3	NFIC	chr2:55281228-55282084	GM12878	blood:	n/a	n/a
4	PAX5	chr2:55281623-55282030	GM12878	blood:	n/a	n/a
5	RUNX3	chr2:55281280-55282015	GM12878	blood:	n/a	n/a
6	BHLHE40	chr2:55281428-55281943	GM12878	blood:	n/a	n/a
7	MEF2A	chr2:55281562-55282062	GM12878	blood:	n/a	n/a
8	STAT1	chr2:55281774-55281977	GM12878	blood:	n/a	n/a
9	TEAD4	chr2:55281516-55282056	ECC-1	luminal epithelium:	n/a	n/a
10	RUNX3	chr2:55281180-55282086	GM12878	blood:	n/a	n/a
11	BATF	chr2:55281645-55282029	GM12878	blood:	n/a	chr2:55281861-55281870
12	RAD21	chr2:55281695-55281995	GM12878	blood:	n/a	n/a
13	NFIC	chr2:55281395-55282102	GM12878	blood:	n/a	n/a
14	FOXM1	chr2:55281486-55282038	GM12878	blood:	n/a	n/a
15	MTA3	chr2:55281501-55282066	GM12878	blood:	n/a	n/a
16	ATF2	chr2:55281235-55282115	GM12878	blood:	n/a	n/a
17	PAX5	chr2:55281640-55281941	GM12878	blood:	n/a	n/a
18	PAX5	chr2:55281688-55281991	GM12878	blood:	n/a	n/a
19	BATF	chr2:55281667-55281969	GM12878	blood:	n/a	chr2:55281861-55281870

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55279956..55282350-chr2:55389384..55392221,3	K562	blood:
2	chr2:55280650..55283253-chr2:55298459..55300307,2	K562	blood:

Variant related genes	Relation type
RTN4	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10173203	0.83[CEU][hapmap];0.88[EUR][1000 genomes]
rs10175952	0.83[YRI][hapmap]
rs10189094	0.84[CEU][hapmap]
rs10206023	0.85[JPT][hapmap]
rs13387836	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3198123	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs3806572	0.84[CEU][hapmap]
rs6705519	0.82[EUR][1000 genomes]
rs6757907	1.00[CEU][hapmap]
rs6760379	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7607923	0.85[JPT][hapmap]

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:54 , 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	chr2:55278600-55282000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr2:55278800-55282200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:55278800-55283200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr2:55278800-55283200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr2:55278800-55288600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:55278800-55290800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:55279000-55282000	Enhancers	Primary B cells from peripheral blood	blood
10	chr2:55279000-55282400	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr2:55279000-55283200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr2:55279000-55287000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr2:55279000-55290600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr2:55279400-55282000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr2:55279400-55282200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr2:55279400-55283000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:55279400-55283200	Weak transcription	Osteobl	bone
18	chr2:55279400-55283400	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr2:55279400-55283400	Weak transcription	Brain Hippocampus Middle	brain
20	chr2:55279400-55287600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr2:55279600-55283000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr2:55279600-55283200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr2:55279800-55282000	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr2:55279800-55282000	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr2:55279800-55282600	Enhancers	Primary B cells from cord blood	blood
26	chr2:55279800-55283200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr2:55279800-55283200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:55279800-55283200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr2:55279800-55283200	Weak transcription	NHDF-Ad	bronchial
30	chr2:55279800-55284200	Weak transcription	Fetal Intestine Small	intestine
31	chr2:55279800-55284400	Weak transcription	Fetal Heart	heart
32	chr2:55279800-55287400	Weak transcription	HSMM	muscle
33	chr2:55280000-55282800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:55280000-55283000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr2:55280000-55283200	Weak transcription	HMEC	breast
36	chr2:55280000-55289000	Weak transcription	HepG2	liver
37	chr2:55280200-55283200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr2:55280200-55283200	Weak transcription	A549	lung
39	chr2:55280200-55287200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr2:55280200-55288200	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr2:55280400-55282800	Enhancers	Fetal Thymus	thymus
42	chr2:55280600-55282000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr2:55280800-55282200	Flanking Active TSS	GM12878-XiMat	blood
44	chr2:55281000-55282000	Enhancers	Placenta Amnion	Placenta Amnion
45	chr2:55281000-55282200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr2:55281400-55282000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr2:55281400-55282000	Enhancers	Fetal Kidney	kidney
48	chr2:55281600-55282000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
49	chr2:55281600-55282000	Flanking Active TSS	Thymus	Thymus
50	chr2:55281800-55282000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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