Variant report

Variant	rs13339257
Chromosome Location	chr16:75352493-75352494
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:75344956..75346715-chr16:75349966..75352704,2	K562	blood:

Extended variants
information (count: 94 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10438605	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11149817	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12149472	0.96[ASN][1000 genomes]
rs12149940	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12444789	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12445803	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12716785	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12918234	0.82[ASN][1000 genomes]
rs12919055	0.86[ASN][1000 genomes]
rs12921808	0.96[ASN][1000 genomes]
rs12926447	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12928461	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12935491	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13337069	0.89[ASN][1000 genomes]
rs17605695	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17674216	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2285221	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2550325	0.96[ASN][1000 genomes]
rs2550916	0.96[ASN][1000 genomes]
rs2650408	0.96[ASN][1000 genomes]
rs2650409	0.96[ASN][1000 genomes]
rs28368934	0.87[ASN][1000 genomes]
rs28510780	0.89[ASN][1000 genomes]
rs28525459	0.89[ASN][1000 genomes]
rs34532060	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4081763	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4383172	0.96[ASN][1000 genomes]
rs55715607	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55719515	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59800961	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60544814	0.89[ASN][1000 genomes]
rs6625	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71380715	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7184596	0.89[ASN][1000 genomes]
rs7185880	0.89[ASN][1000 genomes]
rs7186825	0.89[ASN][1000 genomes]
rs7188111	0.96[ASN][1000 genomes]
rs7189037	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7206589	0.96[ASN][1000 genomes]
rs7206780	0.89[ASN][1000 genomes]
rs729109	0.89[ASN][1000 genomes]
rs8046261	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8047147	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8047983	0.89[ASN][1000 genomes]
rs8048683	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8050367	0.86[ASN][1000 genomes]
rs8051151	0.96[ASN][1000 genomes]
rs8051238	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8052405	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8052555	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8054557	0.86[ASN][1000 genomes]
rs8055098	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8056345	0.96[ASN][1000 genomes]
rs8056473	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8057652	0.89[ASN][1000 genomes]
rs8057925	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8059427	0.89[ASN][1000 genomes]
rs8059883	0.89[ASN][1000 genomes]
rs8060338	0.89[ASN][1000 genomes]
rs8063733	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9319483	0.96[ASN][1000 genomes]
rs9319484	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9745455	0.96[ASN][1000 genomes]
rs9921115	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9921330	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9923034	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9923465	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9923574	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9924524	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9926453	0.86[ASN][1000 genomes]
rs9926933	0.89[ASN][1000 genomes]
rs9927330	0.96[ASN][1000 genomes]
rs9928744	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9928901	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9930002	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9932982	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9935954	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9935967	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9936641	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9936648	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9936853	0.89[ASN][1000 genomes]
rs9937903	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9938936	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9939080	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9939587	0.87[ASN][1000 genomes]
rs9940189	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9940884	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9941142	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9972714	0.90[EUR][1000 genomes];0.96[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13339257	RP11-252K23.2	cis	Esophagus Mucosa	GTEx
rs13339257	RP11-252K23.2	cis	Adipose Subcutaneous	GTEx
rs13339257	RP11-252K23.2	cis	Artery Tibial	GTEx
rs13339257	RP11-252K23.2	cis	Thyroid	GTEx

Chromatin state (count:103 , 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	chr16:75338800-75426400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr16:75339200-75358000	Weak transcription	Brain Germinal Matrix	brain
4	chr16:75339400-75411800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr16:75340000-75353200	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr16:75340200-75353000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr16:75340200-75353200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr16:75340400-75353200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr16:75340400-75374800	Weak transcription	Aorta	Aorta
10	chr16:75340600-75352600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr16:75340600-75352800	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr16:75340600-75353000	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr16:75340600-75354200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr16:75340800-75353600	Weak transcription	Fetal Lung	lung
15	chr16:75340800-75357800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr16:75340800-75373400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr16:75341000-75353000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr16:75341000-75353000	Weak transcription	HSMM	muscle
19	chr16:75341000-75354000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr16:75341000-75354400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr16:75341800-75364600	Weak transcription	Hela-S3	cervix
22	chr16:75342200-75353200	Weak transcription	HMEC	breast
23	chr16:75342200-75357200	Weak transcription	Placenta	Placenta
24	chr16:75342200-75381200	Weak transcription	Esophagus	oesophagus
25	chr16:75342400-75353400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr16:75342400-75354000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr16:75342600-75353400	Weak transcription	NHEK	skin
28	chr16:75342800-75353200	Weak transcription	Fetal Thymus	thymus
29	chr16:75343000-75354400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr16:75344000-75376400	Weak transcription	Gastric	stomach
31	chr16:75344200-75353200	Weak transcription	HSMMtube	muscle
32	chr16:75344600-75354000	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr16:75344600-75361400	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr16:75344800-75359000	Weak transcription	Psoas Muscle	Psoas
35	chr16:75345400-75354000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr16:75345600-75354000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr16:75345600-75357200	Weak transcription	A549	lung
38	chr16:75346000-75353000	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr16:75346000-75354000	Weak transcription	Rectal Smooth Muscle	rectum
40	chr16:75346200-75354000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr16:75346800-75353200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr16:75347200-75353400	Weak transcription	Brain Anterior Caudate	brain
43	chr16:75347200-75353800	Strong transcription	Fetal Intestine Small	intestine
44	chr16:75347400-75353400	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr16:75347600-75353400	Weak transcription	Brain Cingulate Gyrus	brain
46	chr16:75347600-75358200	Weak transcription	Fetal Brain Female	brain
47	chr16:75347600-75366000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr16:75347800-75357800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr16:75348000-75353400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr16:75348400-75353400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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