Variant report

Variant	rs2546206
Chromosome Location	chr5:118813799-118813800
allele	A/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	GATA3	chr5:118813764-118813945	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:118804681..118808687-chr5:118810812..118814012,4	K562	blood:

Variant related genes	Relation type
HSD17B4	TF binding region
ENSG00000239084	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1143650	0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2431545	0.85[AFR][1000 genomes]
rs2546207	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2546208	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2546209	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2546212	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2560719	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2560720	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2560721	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2560722	0.91[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2560724	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2636960	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2636965	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2636967	0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2636970	0.92[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2652698	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2678068	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2678069	0.93[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2678072	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2678073	1.00[AMR][1000 genomes]
rs2678075	0.93[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2678077	0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2678082	1.00[AMR][1000 genomes]
rs2678083	0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2678093	0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34053410	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35121430	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6869575	0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030717	chr5:118709310-118836951	Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv427732	chr5:118730999-119034741	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1024455	chr5:118770429-119487982	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118789000-118826800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr5:118789400-118831200	Weak transcription	NH-A	brain
3	chr5:118789400-118831600	Weak transcription	HSMMtube	muscle
4	chr5:118789800-118813800	Weak transcription	Fetal Kidney	kidney
5	chr5:118789800-118814400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr5:118791800-118846600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:118792400-118815000	Weak transcription	K562	blood
8	chr5:118794800-118861200	Weak transcription	HSMM	muscle
9	chr5:118804200-118879600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr5:118804400-118820000	Weak transcription	NHDF-Ad	bronchial
11	chr5:118804600-118818800	Weak transcription	Stomach Mucosa	stomach
12	chr5:118804600-118819400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr5:118804800-118821400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr5:118804800-118837000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr5:118805200-118839400	Weak transcription	NHEK	skin
16	chr5:118805600-118817200	Weak transcription	Fetal Brain Female	brain
17	chr5:118805800-118817000	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr5:118805800-118829400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr5:118806000-118846400	Weak transcription	Esophagus	oesophagus
20	chr5:118806000-118846400	Weak transcription	Spleen	Spleen
21	chr5:118806200-118831400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr5:118806200-118844800	Weak transcription	Thymus	Thymus
23	chr5:118806200-118846400	Weak transcription	Pancreas	Pancrea
24	chr5:118806200-118855600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr5:118806400-118815200	Weak transcription	Hela-S3	cervix
26	chr5:118806400-118831200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr5:118806400-118845000	Weak transcription	Fetal Stomach	stomach
28	chr5:118806400-118846400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr5:118806600-118814600	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr5:118806600-118832000	Weak transcription	HUVEC	blood vessel
31	chr5:118806800-118845400	Weak transcription	Fetal Heart	heart
32	chr5:118808000-118815800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr5:118808000-118839600	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr5:118808000-118839800	Weak transcription	Psoas Muscle	Psoas
35	chr5:118808200-118815800	Strong transcription	Primary B cells from peripheral blood	blood
36	chr5:118808200-118816200	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr5:118808400-118815000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr5:118808400-118816000	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr5:118809400-118815800	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr5:118809600-118816000	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr5:118809600-118818200	Strong transcription	Liver	Liver
42	chr5:118809600-118838000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr5:118810600-118815200	Strong transcription	Osteobl	bone
44	chr5:118810600-118823200	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr5:118811200-118815800	Strong transcription	Primary B cells from cord blood	blood
46	chr5:118811200-118839600	Weak transcription	Brain Germinal Matrix	brain
47	chr5:118811400-118815600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr5:118811800-118814000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr5:118811800-118815600	Strong transcription	Primary T cells from cord blood	blood
50	chr5:118811800-118816000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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