Variant report

Variant	rs2280601
Chromosome Location	chr7:99056099-99056100
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:99035355..99037078-chr7:99054740..99056500,2	MCF-7	breast:
2	chr7:99051000..99053656-chr7:99053933..99057442,4	MCF-7	breast:
3	chr7:99055017..99057368-chr7:99068752..99070455,3	K562	blood:
4	chr7:99054140..99056503-chr7:99161900..99164159,2	K562	blood:
5	chr7:99055033..99067556-chr7:99095016..99105645,21	K562	blood:
6	chr7:99055033..99057079-chr7:99102410..99104111,3	K562	blood:
7	chr7:99014517..99016789-chr7:99055086..99057589,2	K562	blood:

Variant related genes	Relation type
ENSG00000160908	Chromatin interaction
ENSG00000160917	Chromatin interaction
ENSG00000106246	Chromatin interaction
ENSG00000196652	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1011024	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10155966	0.91[ASW][hapmap];0.92[CEU][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes]
rs10225314	0.82[JPT][hapmap]
rs10238965	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10243678	0.91[ASW][hapmap];0.92[CEU][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes]
rs10244158	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10253937	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10254729	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10258757	0.91[ASW][hapmap];0.92[CEU][hapmap];0.80[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap]
rs10270459	0.92[CEU][hapmap];0.84[JPT][hapmap];0.80[AMR][1000 genomes]
rs10270917	0.92[CEU][hapmap];0.80[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap]
rs10271049	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10271582	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10272998	0.82[ASW][hapmap];0.92[CEU][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap]
rs10279308	0.84[CEU][hapmap]
rs1043466	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10464604	0.81[ASN][1000 genomes]
rs11539770	0.81[ASN][1000 genomes]
rs11762273	0.91[ASW][hapmap];0.92[CEU][hapmap];0.80[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.83[TSI][hapmap]
rs11772470	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs11976018	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11978089	0.84[CEU][hapmap]
rs12538826	0.82[ASN][1000 genomes]
rs13227795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13240600	0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13437771	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980307	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003499	0.84[CEU][hapmap]
rs2072181	0.91[ASW][hapmap];0.92[CEU][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes]
rs2240384	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2240385	0.86[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs2272168	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2280600	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286162	0.92[CEU][hapmap]
rs2404324	0.84[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs28457808	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28495024	0.81[AMR][1000 genomes]
rs3137	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34777615	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3779354	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs3800960	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs3801288	0.92[CEU][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap]
rs3843540	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3901286	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs45492098	0.81[ASN][1000 genomes]
rs45540134	0.87[ASN][1000 genomes]
rs45622743	0.83[ASN][1000 genomes]
rs4729532	0.83[ASW][hapmap];0.84[CEU][hapmap]
rs58222677	0.84[ASN][1000 genomes]
rs61159815	0.85[ASN][1000 genomes]
rs61402640	0.81[ASN][1000 genomes]
rs61543997	0.81[ASN][1000 genomes]
rs6943920	0.91[ASW][hapmap];0.92[CEU][hapmap];0.83[CHD][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.88[TSI][hapmap]
rs6955490	0.83[ASW][hapmap];0.84[CEU][hapmap]
rs6961634	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs6962772	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7794682	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7794705	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7804551	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs868564	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs883403	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs917154	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs940336	0.86[CHB][hapmap];0.84[JPT][hapmap];0.81[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	esv3433144	chr7:98777878-99060209	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv831069	chr7:98948128-99127584	Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2280601	CYP3A5	cis	parietal	SCAN
rs2280601	ACTL6B	cis	cerebellum	SCAN
rs2280601	GATS	cis	parietal	SCAN
rs2280601	CPSF4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99038000-99061600	Strong transcription	Fetal Stomach	stomach
2	chr7:99038200-99056200	Weak transcription	Fetal Heart	heart
3	chr7:99038200-99061800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr7:99038200-99061800	Strong transcription	Fetal Intestine Small	intestine
5	chr7:99038200-99062000	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr7:99038200-99062000	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr7:99038200-99062400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr7:99038400-99062400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr7:99038600-99058000	Strong transcription	NHEK	skin
10	chr7:99038600-99058600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr7:99038600-99062400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr7:99038800-99058000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr7:99039000-99059000	Strong transcription	Fetal Intestine Large	intestine
14	chr7:99039200-99058000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr7:99039200-99058000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr7:99039200-99058200	Strong transcription	Dnd41	blood
17	chr7:99039200-99061600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr7:99039400-99059600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr7:99039600-99058000	Strong transcription	HMEC	breast
20	chr7:99039600-99062000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr7:99040000-99058400	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr7:99040000-99058600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr7:99040000-99059000	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr7:99040000-99060600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr7:99040200-99058200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr7:99040200-99059400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr7:99040200-99059400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr7:99040400-99058200	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr7:99040400-99058400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr7:99040400-99058400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr7:99040400-99058600	Strong transcription	H9 Cell Line	embryonic stem cell
32	chr7:99040400-99058600	Strong transcription	Fetal Lung	lung
33	chr7:99040400-99059000	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr7:99040400-99059600	Strong transcription	Primary T cells from cord blood	blood
35	chr7:99040400-99060800	Strong transcription	Duodenum Mucosa	Duodenum
36	chr7:99040400-99062000	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr7:99040600-99057200	Strong transcription	Ovary	ovary
38	chr7:99040600-99058400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr7:99040800-99062000	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr7:99041000-99057600	Strong transcription	Fetal Brain Female	brain
41	chr7:99041000-99058400	Strong transcription	Liver	Liver
42	chr7:99041000-99058600	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr7:99041000-99058600	Strong transcription	Rectal Mucosa Donor 31	rectum
44	chr7:99041200-99058600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr7:99041400-99058400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr7:99041600-99057400	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr7:99041600-99057800	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr7:99042000-99058000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr7:99042000-99058400	Strong transcription	Fetal Thymus	thymus
50	chr7:99042200-99059200	Strong transcription	GM12878-XiMat	blood

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