Variant report

Variant	rs229651
Chromosome Location	chr14:65206493-65206494
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	POLR2A	chr14:65206362-65206510	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:65205157..65207036-chr14:65211800..65213605,2	MCF-7	breast:
2	chr14:65196332..65199526-chr14:65204522..65207283,4	MCF-7	breast:
3	chr14:65205058..65207899-chr14:65213819..65216284,2	MCF-7	breast:
4	chr14:65170634..65173219-chr14:65206307..65208864,3	MCF-7	breast:

Variant related genes	Relation type
PLEKHG3	TF binding region
ENSG00000126822	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs17179970	0.83[ASN][1000 genomes]
rs17179984	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17180090	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17767188	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17767206	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1985465	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1998120	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs229603	0.88[ASN][1000 genomes]
rs229620	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229624	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs229625	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229626	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229644	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229646	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs229650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229655	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229660	1.00[JPT][hapmap]
rs229662	0.87[ASN][1000 genomes]
rs229663	0.87[ASN][1000 genomes]
rs229664	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs41301473	0.87[ASN][1000 genomes]
rs41307086	0.83[ASN][1000 genomes]
rs58789159	0.87[ASN][1000 genomes]
rs73273524	0.87[ASN][1000 genomes]
rs73273534	0.87[ASN][1000 genomes]
rs73273536	0.87[ASN][1000 genomes]
rs73273546	0.96[ASN][1000 genomes]
rs73273549	0.87[ASN][1000 genomes]
rs754435	0.87[ASN][1000 genomes]
rs872296	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1818582	chr14:65172898-65256685	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1035833	chr14:65176371-65246181	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	esv1801406	chr14:65193725-65264416	Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
4	nsv902023	chr14:65200821-65243885	Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	nsv902024	chr14:65200821-65244950	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65184000-65208800	Weak transcription	Fetal Brain Male	brain
2	chr14:65189800-65207000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr14:65192400-65210400	Weak transcription	Osteobl	bone
4	chr14:65193200-65212200	Weak transcription	Fetal Heart	heart
5	chr14:65193400-65212400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr14:65193400-65212400	Weak transcription	HSMMtube	muscle
7	chr14:65193600-65209200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr14:65193600-65212800	Weak transcription	HUVEC	blood vessel
9	chr14:65193800-65212200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr14:65193800-65214400	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr14:65194000-65209000	Weak transcription	Small Intestine	intestine
12	chr14:65194200-65216200	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr14:65195000-65207200	Weak transcription	Primary B cells from cord blood	blood
14	chr14:65196000-65208200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr14:65196600-65212200	Weak transcription	NHLF	lung
16	chr14:65198000-65214800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr14:65199600-65207800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr14:65200400-65207600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr14:65201000-65221800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr14:65201400-65212600	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr14:65202200-65211200	Strong transcription	Ovary	ovary
22	chr14:65202200-65217400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr14:65202400-65212000	Strong transcription	Stomach Smooth Muscle	stomach
24	chr14:65202600-65211200	Weak transcription	Fetal Thymus	thymus
25	chr14:65202600-65211400	Strong transcription	Rectal Smooth Muscle	rectum
26	chr14:65202800-65207000	Strong transcription	Spleen	Spleen
27	chr14:65202800-65210800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr14:65202800-65211200	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr14:65202800-65211400	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr14:65202800-65211800	Strong transcription	Placenta Amnion	Placenta Amnion
31	chr14:65202800-65212200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr14:65202800-65213000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr14:65202800-65215200	Strong transcription	H9 Cell Line	embryonic stem cell
34	chr14:65203000-65207400	Weak transcription	Hela-S3	cervix
35	chr14:65203000-65211200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr14:65203000-65211400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr14:65203000-65211800	Weak transcription	Primary T cells from cord blood	blood
38	chr14:65203000-65214400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr14:65203200-65211800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr14:65203200-65212000	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr14:65203400-65212000	Strong transcription	Colon Smooth Muscle	Colon
42	chr14:65203600-65212000	Strong transcription	Placenta	Placenta
43	chr14:65203600-65212400	Strong transcription	Brain Inferior Temporal Lobe	brain
44	chr14:65203600-65215000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr14:65203800-65210400	Strong transcription	Fetal Muscle Leg	muscle
46	chr14:65203800-65210800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr14:65203800-65211200	Strong transcription	Adipose Nuclei	Adipose
48	chr14:65203800-65211200	Strong transcription	Gastric	stomach
49	chr14:65203800-65211400	Strong transcription	Lung	lung
50	chr14:65203800-65212200	Strong transcription	HUES6 Cell Line	embryonic stem cell

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