Variant report

Variant	rs229644
Chromosome Location	chr14:65195794-65195795
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:65195242..65196824-chr14:65201352..65202977,2	MCF-7	breast:
2	chr14:65192632..65194965-chr14:65195428..65197963,2	MCF-7	breast:
3	chr14:65168529..65178400-chr14:65179583..65195815,52	MCF-7	breast:
4	chr14:65193907..65195958-chr14:65196523..65198377,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000126822	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

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[CHD][hapmap];1.00[JPT][hapmap]
rs17767188	1.00[CHB][hapmap];1.00[CHD][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	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229621	0.82[GIH][hapmap]
rs229624	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.91[ASN][1000 genomes]
rs229625	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229626	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229646	0.94[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs229650	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229651	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]
rs229655	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229660	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs229662	0.87[ASN][1000 genomes]
rs229663	0.87[ASN][1000 genomes]
rs229664	1.00[CHB][hapmap];1.00[CHD][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:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049097	chr14:65027753-65202018	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs229644	ZBTB1	cis	cerebellum	SCAN
rs229644	PLEKHG3	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65181000-65197600	Enhancers	Primary T helper cells fromperipheralblood	blood
2	chr14:65181200-65197000	Enhancers	Primary T helper cells PMA-I stimulated	--
3	chr14:65183000-65196200	Genic enhancers	Fetal Intestine Small	intestine
4	chr14:65184000-65208800	Weak transcription	Fetal Brain Male	brain
5	chr14:65187000-65197400	Enhancers	Primary T cells from cord blood	blood
6	chr14:65189800-65207000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr14:65191400-65197800	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr14:65191600-65196200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr14:65191600-65198000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr14:65192400-65197600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr14:65192400-65210400	Weak transcription	Osteobl	bone
12	chr14:65192600-65196000	Weak transcription	NHDF-Ad	bronchial
13	chr14:65193000-65197200	Genic enhancers	Fetal Muscle Trunk	muscle
14	chr14:65193200-65200800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr14:65193200-65212200	Weak transcription	Fetal Heart	heart
16	chr14:65193400-65196200	Weak transcription	NHLF	lung
17	chr14:65193400-65198200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr14:65193400-65212400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr14:65193400-65212400	Weak transcription	HSMMtube	muscle
20	chr14:65193600-65198400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr14:65193600-65203200	Strong transcription	Fetal Stomach	stomach
22	chr14:65193600-65209200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr14:65193600-65212800	Weak transcription	HUVEC	blood vessel
24	chr14:65193800-65196000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr14:65193800-65196800	Weak transcription	Fetal Thymus	thymus
26	chr14:65193800-65201200	Strong transcription	Fetal Muscle Leg	muscle
27	chr14:65193800-65212200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr14:65193800-65214400	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr14:65194000-65196600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr14:65194000-65197400	Weak transcription	Hela-S3	cervix
31	chr14:65194000-65198600	Weak transcription	Stomach Mucosa	stomach
32	chr14:65194000-65200600	Strong transcription	A549	lung
33	chr14:65194000-65201200	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr14:65194000-65203000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr14:65194000-65203000	Strong transcription	Placenta	Placenta
36	chr14:65194000-65209000	Weak transcription	Small Intestine	intestine
37	chr14:65194200-65196000	Strong transcription	Esophagus	oesophagus
38	chr14:65194200-65197000	Genic enhancers	Brain Substantia Nigra	brain
39	chr14:65194200-65198600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr14:65194200-65200600	Strong transcription	Colon Smooth Muscle	Colon
41	chr14:65194200-65201000	Strong transcription	Ovary	ovary
42	chr14:65194200-65204800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr14:65194200-65216200	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr14:65194400-65195800	Strong transcription	Left Ventricle	heart
45	chr14:65194400-65195800	Strong transcription	Stomach Smooth Muscle	stomach
46	chr14:65194400-65196000	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr14:65194400-65196200	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr14:65194400-65196200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr14:65194400-65196600	Genic enhancers	Fetal Intestine Large	intestine
50	chr14:65194400-65196600	Enhancers	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links