Variant report

Variant	rs7914996
Chromosome Location	chr10:20113975-20113976
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	chr10:20108456..20110101-chr10:20113566..20116041,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10764159	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10764164	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10827885	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12257233	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1831474	0.82[GIH][hapmap]
rs1977539	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2481936	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2481937	0.88[AFR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2481938	0.88[AFR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2481939	0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2884470	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs333687	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs333689	0.90[EUR][1000 genomes]
rs333691	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs333692	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs420898	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs442830	0.86[EUR][1000 genomes]
rs447706	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4748612	0.98[ASN][1000 genomes]
rs6482065	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7086438	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7094033	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7906452	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7908480	0.84[CHD][hapmap];0.84[GIH][hapmap];0.92[LWK][hapmap];0.85[MKK][hapmap];0.88[YRI][hapmap]
rs7911243	0.81[JPT][hapmap]
rs7912855	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7914865	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9417254	0.82[GIH][hapmap]
rs989767	0.95[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049295	chr10:19740296-20509036	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	esv34306	chr10:19777069-20117944	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1044794	chr10:20010269-20391329	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv540510	chr10:20010269-20391329	Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1038966	chr10:20010469-20391190	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv540511	chr10:20010469-20391190	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1037055	chr10:20010469-20651965	Enhancers Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv540512	chr10:20010469-20651965	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7914996	PLXDC2	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:20107000-20117800	Weak transcription	Spleen	Spleen
2	chr10:20107600-20115800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr10:20107600-20117000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr10:20107600-20117200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr10:20107600-20117600	Weak transcription	Right Ventricle	heart
6	chr10:20107600-20117800	Weak transcription	Fetal Muscle Trunk	muscle
7	chr10:20107600-20121600	Weak transcription	Left Ventricle	heart
8	chr10:20108200-20114600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr10:20108200-20115600	Weak transcription	HMEC	breast
10	chr10:20108200-20117000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr10:20108400-20115800	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr10:20108600-20117000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr10:20108600-20117000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr10:20108600-20117400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr10:20108600-20117600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr10:20108800-20115600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr10:20108800-20117800	Weak transcription	Stomach Smooth Muscle	stomach
18	chr10:20109000-20115800	Weak transcription	Brain Angular Gyrus	brain
19	chr10:20109000-20117000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr10:20109000-20117600	Weak transcription	HSMMtube	muscle
21	chr10:20109200-20115000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr10:20110400-20151400	Weak transcription	Fetal Intestine Small	intestine
23	chr10:20112200-20119800	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr10:20112600-20114200	Enhancers	Brain Hippocampus Middle	brain
25	chr10:20112600-20114200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr10:20112600-20116600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr10:20112600-20117000	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr10:20112800-20114400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr10:20112800-20114800	Enhancers	Brain Substantia Nigra	brain
30	chr10:20112800-20115600	Enhancers	Colon Smooth Muscle	Colon
31	chr10:20112800-20115800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr10:20112800-20115800	Enhancers	Fetal Lung	lung
33	chr10:20113000-20114000	Enhancers	Fetal Kidney	kidney
34	chr10:20113000-20114200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr10:20113000-20114800	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr10:20113000-20114800	Enhancers	Brain Cingulate Gyrus	brain
37	chr10:20113000-20115200	Enhancers	Adipose Nuclei	Adipose
38	chr10:20113000-20119600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr10:20113000-20119800	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr10:20113200-20114400	Enhancers	Brain Anterior Caudate	brain
41	chr10:20113200-20114600	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr10:20113200-20116400	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr10:20113200-20118800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
44	chr10:20113200-20119400	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr10:20113400-20114200	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr10:20113400-20114600	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr10:20113400-20115200	Enhancers	Primary hematopoietic stem cells	blood
48	chr10:20113600-20114000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr10:20113600-20114000	Weak transcription	Fetal Stomach	stomach
50	chr10:20113600-20115400	Weak transcription	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links