Variant report

Variant	rs1772189
Chromosome Location	chr10:93629499-93629500
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:93627211..93629646-chr10:93632804..93634788,2	MCF-7	breast:
2	chr10:93623670..93626355-chr10:93627411..93630158,2	MCF-7	breast:
3	chr10:93627568..93629782-chr10:93667087..93669916,2	MCF-7	breast:
4	chr10:93628714..93630767-chr10:93634147..93636054,2	K562	blood:
5	chr10:93576673..93578768-chr10:93627898..93630166,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174721	Chromatin interaction
ENSG00000272817	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10509634	0.82[JPT][hapmap]
rs10881966	0.82[JPT][hapmap]
rs10881967	0.85[JPT][hapmap]
rs10881973	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10881974	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10881978	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10881979	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10881987	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10881988	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11186696	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11186719	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11186721	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11186722	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11186723	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11598220	0.85[JPT][hapmap]
rs12253245	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1539042	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1592050	0.85[JPT][hapmap]
rs1770466	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1770476	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1772179	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1772182	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1772183	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1890896	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2153655	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2259305	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2275646	0.84[JPT][hapmap]
rs2421698	0.84[JPT][hapmap]
rs2994393	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3802650	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4611111	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4612711	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4933698	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7069232	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7072165	0.84[JPT][hapmap]
rs7076618	0.84[JPT][hapmap]
rs7076687	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7079479	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7096581	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7895548	0.85[JPT][hapmap]
rs7901710	0.82[EUR][1000 genomes]
rs7917858	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv7491	chr10:93626192-93671694	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv511445	chr10:93627158-93635541	Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1772189	TNKS2-AS1	cis	Artery Tibial	GTEx
rs1772189	TNKS2-AS1	cis	Muscle Skeletal	GTEx
rs1772189	TNKS2-AS1	cis	lung	GTEx
rs1772189	TNKS2-AS1	cis	Skin Sun Exposed Lower leg	GTEx
rs1772189	TNKS2-AS1	cis	Adipose Subcutaneous	GTEx
rs1772189	TNKS2-AS1	cis	Esophagus Mucosa	GTEx
rs1772189	TNKS2-AS1	cis	Thyroid	GTEx
rs1772189	TNKS2-AS1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:93599600-93634600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr10:93606400-93630200	Weak transcription	Esophagus	oesophagus
3	chr10:93608800-93639200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr10:93608800-93643400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr10:93618400-93639400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr10:93620600-93631000	Weak transcription	HepG2	liver
7	chr10:93622600-93639000	Weak transcription	Brain Germinal Matrix	brain
8	chr10:93622800-93639200	Weak transcription	Brain Angular Gyrus	brain
9	chr10:93624200-93630200	Weak transcription	Brain Anterior Caudate	brain
10	chr10:93624200-93634400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr10:93624200-93639200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr10:93625800-93632200	Weak transcription	HSMM	muscle
13	chr10:93625800-93634400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr10:93625800-93639000	Weak transcription	Fetal Brain Female	brain
15	chr10:93626000-93629800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr10:93626200-93630000	Weak transcription	NHEK	skin
17	chr10:93626200-93630200	Weak transcription	Adipose Nuclei	Adipose
18	chr10:93626200-93634800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr10:93626200-93639600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr10:93626200-93643000	Weak transcription	HSMMtube	muscle
21	chr10:93627000-93634400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr10:93627600-93639000	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr10:93627600-93639600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr10:93627800-93639000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr10:93628600-93629600	Enhancers	H1 Cell Line	embryonic stem cell
26	chr10:93628600-93629800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr10:93628800-93629600	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr10:93628800-93629600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr10:93629000-93629600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
30	chr10:93629000-93629600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr10:93629000-93629600	Enhancers	H9 Cell Line	embryonic stem cell
32	chr10:93629000-93629600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr10:93629200-93631600	Weak transcription	Placenta	Placenta
34	chr10:93629400-93629600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links