Variant report

Variant	rs17177802
Chromosome Location	chr14:71632302-71632303
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:71631309..71633976-chr14:71786806..71788570,3	MCF-7	breast:
2	chr14:71630664..71636301-chr14:71785635..71788811,7	MCF-7	breast:
3	chr14:71536680..71538584-chr14:71630559..71632306,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197555	Chromatin interaction
ENSG00000259146	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10162332	1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10162513	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1017023	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1017024	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11158894	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11158895	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11622578	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11628267	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12433285	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12433881	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12433971	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12436140	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12436994	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12437099	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12586505	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12591005	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17767137	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2003488	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2079305	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55831429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55968807	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55979041	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56369736	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7144242	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7152112	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72726621	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72726627	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72726634	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs740069	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs740070	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs740071	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs740072	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs917063	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][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	nsv1041980	chr14:71196358-71767339	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv542125	chr14:71196358-71767339	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1038007	chr14:71269747-71667680	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv1036929	chr14:71469148-71683412	Strong transcription Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1044090	chr14:71496198-71780026	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17177802	PCNX	cis	parietal	SCAN
rs17177802	PCNX	cis	cerebellum	SCAN
rs17177802	TTC9	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71629400-71632800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr14:71629400-71633400	Enhancers	Fetal Intestine Small	intestine
3	chr14:71629400-71633800	Enhancers	Liver	Liver
4	chr14:71629600-71632600	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr14:71629600-71633600	Enhancers	Fetal Intestine Large	intestine
6	chr14:71630200-71633000	Enhancers	Colonic Mucosa	Colon
7	chr14:71630400-71633000	Enhancers	Pancreas	Pancrea
8	chr14:71630400-71633200	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr14:71630400-71633800	Enhancers	Fetal Kidney	kidney
10	chr14:71630600-71633400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr14:71630600-71633600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr14:71631000-71633400	Enhancers	Placenta	Placenta
13	chr14:71631200-71633000	Enhancers	Fetal Muscle Leg	muscle
14	chr14:71631400-71632600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr14:71631400-71632600	Enhancers	Fetal Heart	heart
16	chr14:71631400-71633200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr14:71631400-71633400	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr14:71631600-71632400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr14:71631600-71632400	Enhancers	Fetal Muscle Trunk	muscle
20	chr14:71631600-71632600	Enhancers	HMEC	breast
21	chr14:71631600-71632600	Enhancers	HSMM	muscle
22	chr14:71631600-71632600	Enhancers	HSMMtube	muscle
23	chr14:71631600-71633000	Enhancers	Fetal Lung	lung
24	chr14:71631600-71633200	Enhancers	NHEK	skin
25	chr14:71631600-71633400	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr14:71631600-71636600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr14:71631800-71632400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr14:71631800-71632400	Enhancers	Adipose Nuclei	Adipose
29	chr14:71631800-71632400	Enhancers	Lung	lung
30	chr14:71631800-71632400	Enhancers	Placenta Amnion	Placenta Amnion
31	chr14:71631800-71632600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr14:71631800-71632600	Active TSS	Rectal Mucosa Donor 29	rectum
33	chr14:71631800-71632600	Enhancers	Osteobl	bone
34	chr14:71631800-71632800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr14:71631800-71633400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr14:71631800-71633400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr14:71631800-71633400	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr14:71631800-71633800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr14:71631800-71636600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr14:71632000-71632400	Enhancers	Stomach Mucosa	stomach
41	chr14:71632000-71632600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr14:71632000-71632600	Active TSS	Rectal Smooth Muscle	rectum
43	chr14:71632000-71632600	Enhancers	Right Atrium	heart
44	chr14:71632000-71633000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr14:71632000-71633000	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr14:71632200-71632400	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr14:71632200-71632600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr14:71632200-71632600	Flanking Active TSS	Duodenum Mucosa	Duodenum
49	chr14:71632200-71636600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links