Variant report

Variant	rs9923574
Chromosome Location	chr16:75346240-75346241
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:75341957..75345575-chr16:75345642..75348406,3	MCF-7	breast:
2	chr16:75339387..75342479-chr16:75344631..75347151,3	MCF-7	breast:
3	chr16:75343410..75346715-chr16:75348613..75350936,4	MCF-7	breast:
4	chr16:75297827..75300286-chr16:75345061..75347148,2	K562	blood:
5	chr16:75337884..75341581-chr16:75345017..75347535,3	K562	blood:
6	chr16:75291273..75292814-chr16:75345421..75347980,2	MCF-7	breast:
7	chr16:75342449..75344190-chr16:75344958..75347399,2	K562	blood:
8	chr16:75344956..75346715-chr16:75349966..75352704,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000050820	Chromatin interaction
ENSG00000153774	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10438605	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11149817	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12149472	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12149940	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12444789	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12445803	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12716785	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12918234	0.86[ASN][1000 genomes]
rs12919055	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12921808	1.00[ASN][1000 genomes]
rs12926447	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12928461	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12935491	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13337069	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13339257	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17605695	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17674216	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2285221	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2550325	1.00[ASN][1000 genomes]
rs2550916	1.00[ASN][1000 genomes]
rs2650408	1.00[ASN][1000 genomes]
rs2650409	1.00[ASN][1000 genomes]
rs28368934	0.90[ASN][1000 genomes]
rs28371085	0.85[EUR][1000 genomes]
rs28510780	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28525459	0.93[ASN][1000 genomes]
rs34532060	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35255668	0.87[EUR][1000 genomes]
rs4081763	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4383172	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55715607	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55719515	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59800961	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60544814	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6625	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71380715	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7184596	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7185880	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7186825	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7188111	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7189037	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7206589	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7206780	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs729109	0.93[ASN][1000 genomes]
rs8046261	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8047147	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8047983	0.93[ASN][1000 genomes]
rs8048683	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8050367	0.89[ASN][1000 genomes]
rs8051151	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8051238	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8052405	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8052555	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8054557	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8055098	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8056345	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8056473	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8057652	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8057925	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8059427	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8059883	0.93[ASN][1000 genomes]
rs8060338	0.93[ASN][1000 genomes]
rs8063733	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9319483	1.00[ASN][1000 genomes]
rs9319484	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9745455	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9921115	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9921330	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9923034	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9923465	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9924524	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9926453	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9926933	0.93[ASN][1000 genomes]
rs9927330	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9928744	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9928901	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9930002	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9932982	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9935954	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9935967	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9936641	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9936648	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9936853	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9937903	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9938936	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9939080	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9939587	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9940189	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9940884	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9941142	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9972714	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv1061095	chr16:74519718-75407020	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv532560	chr16:74692406-75411912	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
3	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
4	nsv931939	chr16:75261354-75765025	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
5	nsv833283	chr16:75302175-75392308	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9923574	RP11-252K23.2	cis	Artery Tibial	GTEx
rs9923574	RP11-252K23.2	cis	Esophagus Mucosa	GTEx
rs9923574	RP11-252K23.2	cis	Nerve Tibial	GTEx
rs9923574	RP11-252K23.2	cis	Thyroid	GTEx
rs9923574	RP11-252K23.2	cis	lung	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75317400-75358000	Weak transcription	Fetal Brain Male	brain
2	chr16:75332600-75352000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr16:75335000-75346400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr16:75336000-75346600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr16:75336800-75346600	Weak transcription	Ovary	ovary
6	chr16:75338800-75346600	Weak transcription	Fetal Brain Female	brain
7	chr16:75338800-75349400	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr16:75338800-75349800	Weak transcription	Primary B cells from peripheral blood	blood
9	chr16:75338800-75351200	Weak transcription	Right Ventricle	heart
10	chr16:75338800-75426400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr16:75339000-75346800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr16:75339000-75347000	Weak transcription	Lung	lung
13	chr16:75339200-75358000	Weak transcription	Brain Germinal Matrix	brain
14	chr16:75339400-75411800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr16:75339800-75346800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr16:75339800-75347000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr16:75339800-75347000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr16:75340000-75353200	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr16:75340200-75353000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr16:75340200-75353200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr16:75340400-75346800	Weak transcription	Adipose Nuclei	Adipose
22	chr16:75340400-75347400	Weak transcription	Thymus	Thymus
23	chr16:75340400-75349600	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr16:75340400-75351000	Weak transcription	GM12878-XiMat	blood
25	chr16:75340400-75353200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr16:75340400-75374800	Weak transcription	Aorta	Aorta
27	chr16:75340600-75346400	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr16:75340600-75347800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr16:75340600-75352600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr16:75340600-75352800	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr16:75340600-75353000	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr16:75340600-75354200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr16:75340800-75346800	Weak transcription	Primary T cells from cord blood	blood
34	chr16:75340800-75346800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr16:75340800-75347400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr16:75340800-75351000	Weak transcription	Left Ventricle	heart
37	chr16:75340800-75353600	Weak transcription	Fetal Lung	lung
38	chr16:75340800-75357800	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr16:75340800-75373400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr16:75341000-75346600	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr16:75341000-75346600	Weak transcription	Brain Anterior Caudate	brain
42	chr16:75341000-75346600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr16:75341000-75346800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr16:75341000-75351000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr16:75341000-75353000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr16:75341000-75353000	Weak transcription	HSMM	muscle
47	chr16:75341000-75354000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr16:75341000-75354400	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr16:75341800-75364600	Weak transcription	Hela-S3	cervix
50	chr16:75342200-75346600	Weak transcription	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links