Variant report

Variant	rs4965217
Chromosome Location	chr15:99719773-99719774
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:99660192..99663154-chr15:99718347..99720346,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10902539	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12907394	0.86[ASW][hapmap];0.82[CHD][hapmap]
rs12915090	0.86[ASW][hapmap];0.82[YRI][hapmap]
rs1567416	0.86[ASW][hapmap]
rs1670213	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1670216	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1670224	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1670230	0.95[CEU][hapmap];0.81[CHB][hapmap];0.83[EUR][1000 genomes]
rs1703761	0.90[CHD][hapmap]
rs1703762	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1703763	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1703765	0.81[CHB][hapmap]
rs1703766	1.00[CEU][hapmap];0.81[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1703771	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs187755	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1976589	0.86[ASW][hapmap]
rs260114	1.00[CEU][hapmap];0.89[GIH][hapmap];0.81[MEX][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2602015	0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs2602016	0.86[ASW][hapmap];0.95[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2602018	0.86[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2602020	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2602022	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2602025	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2602026	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2602030	0.87[ASW][hapmap]
rs2602031	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2602035	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2602036	0.86[ASW][hapmap]
rs2602038	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2623185	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2623188	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2623189	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2623190	0.95[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2623191	0.95[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2924346	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3210942	0.86[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap];0.85[AMR][1000 genomes]
rs4602019	0.81[CEU][hapmap];1.00[YRI][hapmap]
rs4965224	0.86[ASW][hapmap]
rs6598224	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6598225	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7163625	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7164003	0.86[ASW][hapmap]
rs7183226	0.87[CHD][hapmap]
rs9920418	0.86[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531079	chr15:98907913-99878547	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv1039575	chr15:98982045-99924685	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv869529	chr15:99416774-99903351	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv1050982	chr15:99450004-99725825	Enhancers Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv1045124	chr15:99504843-99847210	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv1038870	chr15:99510479-99768374	Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv904543	chr15:99513231-99991506	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
9	nsv533926	chr15:99519820-99997114	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
10	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
11	nsv1051782	chr15:99621061-99792967	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
12	nsv916822	chr15:99621061-99878564	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
13	nsv949203	chr15:99621061-99932797	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
14	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
15	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
16	nsv570716	chr15:99629901-99916332	Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
17	nsv904546	chr15:99696046-100166300	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats 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	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4965217	TTC23	cis	multi-tissue	Pritchard
rs4965217	TTC23	cis	parietal	SCAN
rs4965217	TTC23	cis	cerebellum	SCAN
rs4965217	SYNM	cis	parietal	SCAN
rs4965217	SYNM	cis	cerebellum	SCAN
rs4965217	NR2F2	cis	parietal	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99673200-99789400	Weak transcription	Small Intestine	intestine
2	chr15:99684800-99721600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr15:99685000-99720200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr15:99694800-99721200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr15:99694800-99732600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:99694800-99732600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr15:99695200-99721600	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr15:99695200-99721800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr15:99695200-99732400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr15:99697000-99756400	Weak transcription	Stomach Mucosa	stomach
11	chr15:99699400-99731400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr15:99700200-99731200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr15:99700400-99730600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr15:99703400-99728200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr15:99705000-99732400	Weak transcription	Fetal Kidney	kidney
16	chr15:99709400-99732600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr15:99709600-99731400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr15:99709600-99732600	Weak transcription	GM12878-XiMat	blood
19	chr15:99709800-99732600	Weak transcription	Spleen	Spleen
20	chr15:99710000-99721000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr15:99710200-99724000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr15:99710400-99732400	Weak transcription	Fetal Brain Female	brain
23	chr15:99711200-99720000	Weak transcription	Brain Anterior Caudate	brain
24	chr15:99711400-99730800	Weak transcription	Duodenum Mucosa	Duodenum
25	chr15:99711600-99721400	Weak transcription	NHLF	lung
26	chr15:99711600-99725000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr15:99711600-99738600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr15:99711800-99732200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr15:99712800-99731600	Weak transcription	Colonic Mucosa	Colon
30	chr15:99713600-99720000	Weak transcription	HepG2	liver
31	chr15:99713600-99721000	Weak transcription	A549	lung
32	chr15:99714000-99720400	Weak transcription	HSMMtube	muscle
33	chr15:99714400-99721600	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr15:99714400-99724000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr15:99714400-99725000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr15:99714600-99721600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr15:99715000-99721800	Weak transcription	Osteobl	bone
38	chr15:99715200-99725600	Weak transcription	NH-A	brain
39	chr15:99715400-99720000	Weak transcription	Brain Angular Gyrus	brain
40	chr15:99715400-99721000	Weak transcription	Dnd41	blood
41	chr15:99715400-99721600	Weak transcription	Aorta	Aorta
42	chr15:99715400-99724200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr15:99715400-99731400	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr15:99715600-99724000	Weak transcription	Fetal Intestine Large	intestine
45	chr15:99715600-99732600	Weak transcription	Pancreas	Pancrea
46	chr15:99715600-99732600	Weak transcription	NHEK	skin
47	chr15:99715600-99738600	Weak transcription	Hela-S3	cervix
48	chr15:99715800-99719800	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr15:99715800-99720000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr15:99715800-99720000	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links