Variant report

Variant	rs17156041
Chromosome Location	chr7:27975745-27975746
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:27779003..27781367-chr7:27974621..27976627,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229893	Chromatin interaction
ENSG00000106052	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10486567	0.90[CEU][hapmap];0.88[GIH][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes]
rs10807843	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11971132	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11982766	0.95[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2040668	0.86[CEU][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67152137	0.91[EUR][1000 genomes]
rs67746093	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs739704	0.82[CEU][hapmap]
rs757136	0.95[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7808935	0.90[CEU][hapmap];0.91[EUR][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	nsv949025	chr7:27578167-28075172	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1030685	chr7:27844038-28177301	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1024819	chr7:27949955-28020969	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17156041	HOXA13	cis	parietal	SCAN
rs17156041	CAPS	trans	cerebellum	SCAN
rs17156041	CYCS	cis	cerebellum	SCAN
rs17156041	CYCS	cis	parietal	SCAN
rs17156041	CRHR2	cis	parietal	SCAN
rs17156041	TRIL	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27941400-27990800	Weak transcription	Primary T cells from cord blood	blood
2	chr7:27942400-28005600	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr7:27956600-27979800	Weak transcription	Aorta	Aorta
4	chr7:27957200-27979000	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr7:27957600-28000800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr7:27961000-27976000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr7:27961000-27983400	Weak transcription	NH-A	brain
8	chr7:27963400-27978000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr7:27963600-27976400	Weak transcription	Psoas Muscle	Psoas
10	chr7:27964000-27979200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr7:27966400-27976600	Weak transcription	Primary B cells from cord blood	blood
12	chr7:27968400-27979000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr7:27970000-27980000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr7:27972000-27977400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr7:27972200-27975800	Enhancers	NHDF-Ad	bronchial
16	chr7:27972600-27979200	Weak transcription	Primary B cells from peripheral blood	blood
17	chr7:27972800-27979000	Weak transcription	Fetal Stomach	stomach
18	chr7:27973400-27976200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr7:27973600-27979000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr7:27973600-27982600	Weak transcription	Spleen	Spleen
21	chr7:27973800-27975800	Weak transcription	Colon Smooth Muscle	Colon
22	chr7:27973800-27976200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr7:27973800-27978600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr7:27973800-27979200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr7:27973800-27986200	Weak transcription	HSMM	muscle
26	chr7:27974000-27976000	Weak transcription	A549	lung
27	chr7:27974000-27979200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr7:27974000-27980800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr7:27974000-27981200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr7:27974000-27981400	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr7:27974000-27990800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr7:27974400-27980200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr7:27975200-27976600	Enhancers	Fetal Lung	lung
34	chr7:27975400-27975800	Enhancers	Left Ventricle	heart
35	chr7:27975400-27976400	Enhancers	Fetal Muscle Leg	muscle
36	chr7:27975400-27977000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr7:27975400-27977000	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr7:27975400-27977400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr7:27975600-27977000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr7:27975600-27977000	Enhancers	Fetal Heart	heart
41	chr7:27975600-27981000	Weak transcription	Adipose Nuclei	Adipose
42	chr7:27975600-27984800	Weak transcription	Fetal Muscle Trunk	muscle

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