Variant report

Variant	rs2245659
Chromosome Location	chr7:103844557-103844558
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:103844120..103846835-chr7:103848105..103849807,2	MCF-7	breast:
2	chr7:103839347..103842114-chr7:103842519..103845580,4	K562	blood:

Variant related genes	Relation type
ENSG00000164815	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1035169	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10808128	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10953408	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs113877	0.84[ASN][1000 genomes]
rs12056186	0.94[ASN][1000 genomes]
rs12056191	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12705180	0.81[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12705181	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12705184	0.81[ASN][1000 genomes]
rs12705187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12705188	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs12705190	0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12705192	0.80[JPT][hapmap]
rs12705193	0.81[EUR][1000 genomes]
rs12705195	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13230700	1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13238183	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs193888	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs194837	0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs194838	0.83[ASN][1000 genomes]
rs194841	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[ASN][1000 genomes]
rs194846	0.91[ASW][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[YRI][hapmap];0.84[ASN][1000 genomes]
rs194847	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs194849	0.82[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.80[MKK][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs194851	0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs194857	0.91[ASW][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.92[YRI][hapmap];0.84[ASN][1000 genomes]
rs194858	0.81[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs194859	0.85[CEU][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs194861	0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs194865	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs194867	0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs194868	0.82[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.80[MKK][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2160397	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2283035	0.81[EUR][1000 genomes]
rs2299408	0.85[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2299409	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2299411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2385140	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35034355	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757734	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3779518	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3808008	0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3808009	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3808010	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3823979	0.84[ASN][1000 genomes]
rs4140860	0.95[ASN][1000 genomes]
rs4265123	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4265124	0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs4385404	0.90[ASN][1000 genomes]
rs4461830	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62485910	0.93[ASN][1000 genomes]
rs6948583	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6961262	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6967757	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs765408	0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs7781828	0.94[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	nsv1019640	chr7:103813522-103884705	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
2	nsv1026481	chr7:103813522-103890770	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
3	esv2762692	chr7:103813522-103890782	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
4	nsv526062	chr7:103817597-103891085	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
5	nsv608065	chr7:103817597-103990755	Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2245659	STAP1	trans	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:103797200-103847000	Weak transcription	Fetal Heart	heart
2	chr7:103816000-103846200	Weak transcription	Stomach Mucosa	stomach
3	chr7:103822000-103845400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr7:103826800-103844600	Strong transcription	Adipose Nuclei	Adipose
5	chr7:103827400-103844600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr7:103832800-103846600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr7:103833800-103844800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr7:103834400-103844600	Strong transcription	Liver	Liver
9	chr7:103834600-103844600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr7:103834800-103844600	Strong transcription	Stomach Smooth Muscle	stomach
11	chr7:103836800-103844800	Strong transcription	A549	lung
12	chr7:103837200-103844600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr7:103837200-103844600	Strong transcription	Brain Inferior Temporal Lobe	brain
14	chr7:103838000-103844600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr7:103838400-103844600	Strong transcription	Brain Substantia Nigra	brain
16	chr7:103838400-103844800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr7:103839000-103844600	Strong transcription	HMEC	breast
18	chr7:103839200-103844600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr7:103839400-103844600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr7:103839600-103844600	Strong transcription	Brain Anterior Caudate	brain
21	chr7:103839800-103844600	Strong transcription	Hela-S3	cervix
22	chr7:103839800-103847400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr7:103840000-103844600	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr7:103840000-103844600	Strong transcription	Primary B cells from peripheral blood	blood
25	chr7:103840000-103844600	Strong transcription	HUVEC	blood vessel
26	chr7:103840000-103844800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr7:103840000-103845000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr7:103840000-103847200	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr7:103840000-103847600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr7:103840200-103844600	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr7:103840200-103844800	Strong transcription	NHDF-Ad	bronchial
32	chr7:103840400-103844600	Strong transcription	Primary hematopoietic stem cells	blood
33	chr7:103840400-103847800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr7:103840600-103844600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr7:103840600-103844800	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr7:103840600-103847800	Weak transcription	Small Intestine	intestine
37	chr7:103840800-103844800	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr7:103841000-103844600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr7:103841000-103844600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr7:103841000-103844800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr7:103841000-103846200	Weak transcription	NHLF	lung
42	chr7:103841800-103844600	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr7:103841800-103844600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr7:103841800-103844800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr7:103841800-103844800	Strong transcription	K562	blood
46	chr7:103841800-103846800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr7:103841800-103846800	Weak transcription	Fetal Intestine Small	intestine
48	chr7:103842000-103844600	Strong transcription	Dnd41	blood
49	chr7:103842000-103844800	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr7:103842400-103847200	Weak transcription	HSMMtube	muscle

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