Variant report

Variant	rs10179594
Chromosome Location	chr2:55281435-55281436
allele	G/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	NFIC	chr2:55281228-55282084	GM12878	blood:	n/a	n/a
2	POLR2A	chr2:55281364-55281561	K562	blood:	n/a	n/a
3	RUNX3	chr2:55281280-55282015	GM12878	blood:	n/a	n/a
4	BHLHE40	chr2:55281428-55281943	GM12878	blood:	n/a	n/a
5	RUNX3	chr2:55281180-55282086	GM12878	blood:	n/a	n/a
6	NFIC	chr2:55281395-55282102	GM12878	blood:	n/a	n/a
7	ATF2	chr2:55281235-55282115	GM12878	blood:	n/a	n/a
8	PAX5	chr2:55281202-55281560	GM12892	blood:	n/a	n/a

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: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10196667	0.82[CEU][hapmap];0.82[MEX][hapmap]
rs10205017	0.88[EUR][1000 genomes]
rs10746530	0.82[CEU][hapmap]
rs11125551	0.82[CEU][hapmap]
rs12989576	0.82[CEU][hapmap];0.85[JPT][hapmap];0.90[EUR][1000 genomes]
rs13002841	0.82[CEU][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];0.87[EUR][1000 genomes]
rs13023202	0.89[EUR][1000 genomes]
rs2580763	0.85[JPT][hapmap];0.85[EUR][1000 genomes]
rs2580766	0.82[CEU][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes]
rs2588520	0.82[CEU][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes]
rs2919125	0.82[CEU][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap];0.89[EUR][1000 genomes]
rs2920839	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920861	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2920863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2920881	1.00[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs2920883	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2920884	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2920889	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2920890	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2920897	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2920898	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs2968778	1.00[LWK][hapmap]
rs2968789	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2968792	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2968812	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2968813	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2968814	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2968823	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2968824	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2968826	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2968829	1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs2968831	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2972065	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2972066	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2972067	0.81[ASN][1000 genomes]
rs2972069	0.81[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]
rs6545462	0.82[CEU][hapmap]
rs7559248	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10179594	VPS37B	trans	lymphoblastoid	seeQTL
rs10179594	RTN4	cis	Thyroid	GTEx

Chromatin state (count:56 , 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	chr2:55278600-55281600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr2:55278600-55282000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr2:55278800-55282200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr2:55278800-55283200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr2:55278800-55283200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr2:55278800-55288600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:55278800-55290800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:55279000-55282000	Enhancers	Primary B cells from peripheral blood	blood
11	chr2:55279000-55282400	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr2:55279000-55283200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr2:55279000-55287000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr2:55279000-55290600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr2:55279400-55282000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr2:55279400-55282200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr2:55279400-55283000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:55279400-55283200	Weak transcription	Osteobl	bone
19	chr2:55279400-55283400	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr2:55279400-55283400	Weak transcription	Brain Hippocampus Middle	brain
21	chr2:55279400-55287600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr2:55279600-55283000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr2:55279600-55283200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr2:55279800-55282000	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr2:55279800-55282000	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr2:55279800-55282600	Enhancers	Primary B cells from cord blood	blood
27	chr2:55279800-55283200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr2:55279800-55283200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:55279800-55283200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:55279800-55283200	Weak transcription	NHDF-Ad	bronchial
31	chr2:55279800-55284200	Weak transcription	Fetal Intestine Small	intestine
32	chr2:55279800-55284400	Weak transcription	Fetal Heart	heart
33	chr2:55279800-55287400	Weak transcription	HSMM	muscle
34	chr2:55280000-55281600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr2:55280000-55281800	Enhancers	Dnd41	blood
36	chr2:55280000-55282800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr2:55280000-55283000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:55280000-55283200	Weak transcription	HMEC	breast
39	chr2:55280000-55289000	Weak transcription	HepG2	liver
40	chr2:55280200-55281800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr2:55280200-55283200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:55280200-55283200	Weak transcription	A549	lung
43	chr2:55280200-55287200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr2:55280200-55288200	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr2:55280400-55282800	Enhancers	Fetal Thymus	thymus
46	chr2:55280600-55281600	Enhancers	K562	blood
47	chr2:55280600-55282000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr2:55280800-55282200	Flanking Active TSS	GM12878-XiMat	blood
49	chr2:55281000-55281600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:55281000-55281600	Enhancers	Thymus	Thymus

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