Variant report

Variant	rs11621159
Chromosome Location	chr14:65181717-65181718
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr14:65181602-65182584	H1-hESC	embryonic stem cell:	n/a	chr14:65181874-65181885
2	POLR2A	chr14:65181664-65181722	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:65168529..65178400-chr14:65179583..65195815,52	MCF-7	breast:

Variant related genes	Relation type
PLEKHG3	TF binding region
ENSG00000126822	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10138034	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11621379	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11622754	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11625500	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11628301	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12883289	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12884903	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12892852	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12895353	1.00[ASW][hapmap];0.82[CEU][hapmap];0.88[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1553163	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs170683	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs170685	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17767074	1.00[ASW][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes]
rs229622	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229645	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs229648	1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs229649	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229653	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs229656	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34340219	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7140781	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71420472	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs732311	0.82[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9943995	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	nsv1049097	chr14:65027753-65202018	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv1818582	chr14:65172898-65256685	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1035833	chr14:65176371-65246181	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65175200-65181800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr14:65176000-65186400	Weak transcription	Osteobl	bone
3	chr14:65176200-65182000	Weak transcription	Colonic Mucosa	Colon
4	chr14:65176400-65181800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr14:65176400-65182000	Weak transcription	Stomach Mucosa	stomach
6	chr14:65176800-65182000	Weak transcription	Gastric	stomach
7	chr14:65177000-65181800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr14:65177000-65189200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr14:65177200-65183400	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr14:65178000-65181800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr14:65178000-65182000	Weak transcription	Ovary	ovary
12	chr14:65178000-65182000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr14:65178200-65181800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr14:65178200-65182000	Weak transcription	Fetal Stomach	stomach
15	chr14:65178200-65182000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr14:65178200-65182000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr14:65179000-65181800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr14:65179800-65181800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr14:65180200-65181800	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr14:65180400-65181800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr14:65180400-65181800	Weak transcription	Fetal Heart	heart
22	chr14:65180400-65181800	Strong transcription	A549	lung
23	chr14:65180400-65182000	Weak transcription	Fetal Kidney	kidney
24	chr14:65180600-65181800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr14:65180600-65181800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr14:65180800-65181800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr14:65180800-65182200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr14:65180800-65182200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr14:65180800-65182200	Enhancers	Brain Cingulate Gyrus	brain
30	chr14:65180800-65182200	Genic enhancers	HMEC	breast
31	chr14:65180800-65182400	Enhancers	Brain Angular Gyrus	brain
32	chr14:65180800-65185400	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr14:65181000-65181800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr14:65181000-65182000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr14:65181000-65182000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
36	chr14:65181000-65182000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr14:65181000-65182000	Enhancers	Brain Substantia Nigra	brain
38	chr14:65181000-65182200	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr14:65181000-65182200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr14:65181000-65182200	Genic enhancers	NHEK	skin
41	chr14:65181000-65189400	Enhancers	Primary T cells fromperipheralblood	blood
42	chr14:65181000-65197600	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr14:65181200-65182000	Enhancers	H1 Cell Line	embryonic stem cell
44	chr14:65181200-65182000	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr14:65181200-65182200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr14:65181200-65182400	Enhancers	H9 Cell Line	embryonic stem cell
47	chr14:65181200-65182600	Enhancers	Placenta	Placenta
48	chr14:65181200-65183800	Weak transcription	Hela-S3	cervix
49	chr14:65181200-65184400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr14:65181200-65185800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links