Variant report

Variant	rs2770201
Chromosome Location	chr10:27528256-27528257
allele	C/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	STAT3	chr10:27528160-27528259	MCF10A-Er-Src	breast:	n/a	n/a
2	CEBPB	chr10:27528048-27528279	A549	lung:	n/a	chr10:27528144-27528157

No.	Distal block	Cell Line	Cell type
1	chr10:27441850..27444956-chr10:27527496..27532549,10	MCF-7	breast:
2	chr10:27518617..27521324-chr10:27527252..27530128,4	K562	blood:
3	chr10:27519175..27520963-chr10:27527252..27529084,2	K562	blood:
4	chr10:27523074..27525459-chr10:27528062..27530998,5	K562	blood:
5	chr10:27441114..27446089-chr10:27527560..27532728,23	MCF-7	breast:
6	chr10:27442176..27446829-chr10:27524472..27534671,19	K562	blood:

Variant related genes	Relation type
ENSG00000262412	TF binding region
ENSG00000263577	TF binding region
ENSG00000263577	Chromatin interaction
ENSG00000136758	Chromatin interaction
ENSG00000251839	Chromatin interaction
ENSG00000120539	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs11015613	0.84[EUR][1000 genomes]
rs1144508	0.94[CEU][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1144509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12763511	0.82[EUR][1000 genomes]
rs1618826	0.95[CEU][hapmap];0.88[CHB][hapmap]
rs17531310	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1753387	0.81[EUR][1000 genomes]
rs1753394	0.94[CEU][hapmap];0.88[CHB][hapmap]
rs1775348	0.82[EUR][1000 genomes]
rs1775352	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1775354	0.82[EUR][1000 genomes]
rs1780090	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1780093	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1819352	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1831187	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1831188	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1854340	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1974364	0.81[EUR][1000 genomes]
rs2026015	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2104670	0.84[CEU][hapmap];0.94[CHB][hapmap];0.84[ASN][1000 genomes]
rs2104671	0.84[ASN][1000 genomes]
rs2274636	0.83[CHB][hapmap]
rs2274637	0.83[CHB][hapmap]
rs2368218	0.84[ASN][1000 genomes]
rs2368219	0.87[EUR][1000 genomes]
rs2368221	0.83[CEU][hapmap]
rs2483489	1.00[YRI][hapmap]
rs2483491	0.90[YRI][hapmap]
rs2488368	0.83[ASN][1000 genomes]
rs2488369	0.83[ASN][1000 genomes]
rs2489374	0.83[ASN][1000 genomes]
rs2770200	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2780665	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2780666	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2780668	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2780669	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2780670	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2780671	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2780673	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2780677	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2780678	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2780679	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2797077	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2797079	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2800391	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2800393	0.92[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2800394	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2800395	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2800397	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2800398	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2800399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2800401	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2800402	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2800403	1.00[CEU][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2800404	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2800405	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2800406	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2995499	0.90[YRI][hapmap]
rs35209475	0.92[ASN][1000 genomes]
rs35844030	0.83[CHB][hapmap]
rs3737056	0.82[CHB][hapmap]
rs3758438	0.83[CHB][hapmap]
rs4747589	0.95[CEU][hapmap];0.88[MEX][hapmap]
rs4747595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4749236	0.82[EUR][1000 genomes]
rs4749239	0.84[EUR][1000 genomes]
rs480738	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs484172	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs501495	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs527192	0.86[ASN][1000 genomes]
rs534226	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs559839	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs576161	0.83[ASN][1000 genomes]
rs604705	0.89[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs618050	0.86[ASN][1000 genomes]
rs623380	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs624106	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs640284	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs642428	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs642430	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6482603	0.82[EUR][1000 genomes]
rs7074295	0.82[EUR][1000 genomes]
rs7078662	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7085905	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7477200	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs788201	0.89[CEU][hapmap];0.88[CHB][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap]
rs788202	0.95[CEU][hapmap];0.88[CHB][hapmap]
rs788203	0.95[CEU][hapmap];0.94[CHB][hapmap]
rs788212	1.00[CEU][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs788215	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs788216	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[ASN][1000 genomes]
rs788230	0.84[CEU][hapmap];0.83[CHB][hapmap];0.81[GIH][hapmap]
rs7902034	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7902126	0.82[EUR][1000 genomes]
rs7914155	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7917207	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs944909	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

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	esv2422253	chr10:27431366-27575370	Strong transcription Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3337781	chr10:27472216-27666703	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv8614	chr10:27504487-27828406	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2770201	ACBD5	cis	Thyroid	GTEx
rs2770201	ANKRD26	cis	parietal	SCAN
rs2770201	MASTL	cis	cerebellum	SCAN
rs2770201	KIAA1217	cis	parietal	SCAN
rs2770201	PSMC6	trans	parietal	SCAN
rs2770201	ACBD5	cis	cerebellum	SCAN
rs2770201	MASTL	cis	Artery Tibial	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:27475600-27528600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr10:27476200-27528600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr10:27488600-27528600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr10:27500000-27528400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr10:27508400-27528400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr10:27508600-27529000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr10:27508800-27528600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr10:27508800-27528600	Weak transcription	Esophagus	oesophagus
9	chr10:27508800-27528600	Weak transcription	Thymus	Thymus
10	chr10:27508800-27528600	Weak transcription	HSMMtube	muscle
11	chr10:27508800-27528800	Weak transcription	Aorta	Aorta
12	chr10:27508800-27529000	Weak transcription	Small Intestine	intestine
13	chr10:27516600-27528600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr10:27517000-27528400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr10:27519800-27528600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr10:27519800-27528600	Weak transcription	Gastric	stomach
17	chr10:27520200-27528400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr10:27520400-27528600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr10:27520600-27528600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr10:27520600-27528600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr10:27520800-27528400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr10:27520800-27528600	Weak transcription	Brain Anterior Caudate	brain
23	chr10:27520800-27528600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr10:27520800-27528600	Weak transcription	Placenta	Placenta
25	chr10:27520800-27528600	Weak transcription	HSMM	muscle
26	chr10:27522600-27528600	Weak transcription	Fetal Thymus	thymus
27	chr10:27524000-27528400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr10:27524000-27528600	Weak transcription	Fetal Muscle Leg	muscle
29	chr10:27525000-27528800	Weak transcription	Ovary	ovary
30	chr10:27525000-27529000	Weak transcription	Stomach Mucosa	stomach
31	chr10:27525600-27528600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr10:27526400-27530000	Active TSS	A549	lung
33	chr10:27526600-27528400	Enhancers	Primary T cells fromperipheralblood	blood
34	chr10:27527000-27528400	Enhancers	Primary T helper cells fromperipheralblood	blood
35	chr10:27527200-27528400	Enhancers	HepG2	liver
36	chr10:27527200-27528600	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr10:27527200-27528600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr10:27527200-27528600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr10:27527200-27528600	Weak transcription	Lung	lung
40	chr10:27527400-27528400	Flanking Active TSS	Liver	Liver
41	chr10:27527400-27528600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr10:27527600-27528600	Enhancers	Fetal Heart	heart
43	chr10:27527800-27528400	Enhancers	Primary hematopoietic stem cells	blood
44	chr10:27527800-27528400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr10:27527800-27528400	Genic enhancers	Fetal Stomach	stomach
46	chr10:27527800-27528400	Enhancers	Left Ventricle	heart
47	chr10:27527800-27528400	Flanking Active TSS	Hela-S3	cervix
48	chr10:27527800-27528600	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr10:27527800-27528600	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr10:27527800-27528600	Enhancers	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links