Variant report

Variant	rs4240872
Chromosome Location	chr1:154436195-154436196
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:154425985..154428453-chr1:154436104..154438755,2	MCF-7	breast:
2	chr1:154423682..154425869-chr1:154434875..154437152,2	MCF-7	breast:
3	chr1:154435097..154437712-chr1:154439386..154441987,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160712	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10752641	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908839	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2229238	0.86[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[ASN][1000 genomes]
rs35699331	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811448	0.94[GIH][hapmap];0.82[MEX][hapmap]
rs4072391	0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[ASN][1000 genomes]
rs4291493	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4341355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4379670	0.86[ASN][1000 genomes]
rs4509570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55668699	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6427672	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6674171	0.84[CHD][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap]
rs6687597	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6698040	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514452	0.86[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[ASN][1000 genomes]
rs7537291	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7537316	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7546068	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7546552	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7546555	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7551873	0.84[CHD][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap]
rs7556449	0.84[CHD][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap]

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	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
2	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
3	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4240872	S100A7A	cis	cerebellum	SCAN
rs4240872	PI4KB	cis	parietal	SCAN
rs4240872	TDRD10	cis	lung	GTEx
rs4240872	CDC42SE1	cis	parietal	SCAN
rs4240872	CDC42SE1	cis	cerebellum	SCAN
rs4240872	LINGO4	cis	parietal	SCAN
rs4240872	PMF1	cis	cerebellum	SCAN
rs4240872	ADAMTSL4	cis	parietal	SCAN
rs4240872	PMF1	cis	parietal	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154418000-154440000	Weak transcription	Small Intestine	intestine
2	chr1:154422600-154437600	Weak transcription	Pancreas	Pancrea
3	chr1:154425000-154437200	Weak transcription	Fetal Stomach	stomach
4	chr1:154426000-154436200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr1:154426400-154438000	Weak transcription	Psoas Muscle	Psoas
6	chr1:154426600-154440600	Weak transcription	Brain Angular Gyrus	brain
7	chr1:154426800-154441200	Weak transcription	Brain Substantia Nigra	brain
8	chr1:154426800-154442200	Weak transcription	HepG2	liver
9	chr1:154426800-154450000	Weak transcription	Fetal Intestine Small	intestine
10	chr1:154427800-154464800	Weak transcription	Ovary	ovary
11	chr1:154428600-154437600	Weak transcription	Gastric	stomach
12	chr1:154429800-154446200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr1:154430400-154438800	Weak transcription	Primary B cells from cord blood	blood
14	chr1:154431000-154437400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:154431200-154437600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:154431600-154441400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr1:154431800-154436200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:154432000-154437400	Weak transcription	Left Ventricle	heart
19	chr1:154432000-154437800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr1:154432000-154442000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:154432800-154437400	Enhancers	Primary T cells fromperipheralblood	blood
22	chr1:154434200-154436600	Genic enhancers	Primary monocytes fromperipheralblood	blood
23	chr1:154434400-154436200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:154434400-154438600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr1:154434600-154436200	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr1:154434800-154436600	Genic enhancers	Monocytes-CD14+_RO01746	blood
27	chr1:154434800-154439600	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr1:154435000-154437600	Enhancers	Placenta	Placenta
29	chr1:154435200-154436600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
30	chr1:154435200-154441000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr1:154435400-154436400	Enhancers	HMEC	breast
32	chr1:154435400-154436600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr1:154435400-154436600	Enhancers	Muscle Satellite Cultured Cells	--
34	chr1:154435400-154436600	Enhancers	Adipose Nuclei	Adipose
35	chr1:154435600-154436200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:154435600-154436400	Enhancers	A549	lung
37	chr1:154435600-154436400	Enhancers	NHEK	skin
38	chr1:154435600-154436600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:154435600-154436600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr1:154435600-154436600	Enhancers	Dnd41	blood
41	chr1:154435600-154436600	Enhancers	GM12878-XiMat	blood
42	chr1:154435600-154436600	Enhancers	HUVEC	blood vessel
43	chr1:154435600-154436600	Enhancers	K562	blood
44	chr1:154435600-154436600	Enhancers	NHDF-Ad	bronchial
45	chr1:154435600-154436800	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr1:154435600-154437800	Enhancers	Stomach Mucosa	stomach
47	chr1:154435600-154440000	Enhancers	Primary hematopoietic stem cells	blood
48	chr1:154435600-154441400	Enhancers	Fetal Thymus	thymus
49	chr1:154435800-154436200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:154435800-154436200	Enhancers	HUES6 Cell Line	embryonic stem cell

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