Variant report

Variant	rs8023816
Chromosome Location	chr15:57288766-57288767
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11071303	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11856411	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12901355	0.84[EUR][1000 genomes]
rs1430820	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1430822	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16977153	0.85[ASN][1000 genomes]
rs16977222	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17415731	0.97[ASN][1000 genomes]
rs1820994	0.86[ASN][1000 genomes]
rs28360967	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28422021	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28505122	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28533433	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28541606	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28612876	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28616268	0.85[EUR][1000 genomes]
rs28648577	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28649108	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28654848	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28677775	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28756149	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28814080	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28856894	0.88[EUR][1000 genomes]
rs4774245	0.85[ASN][1000 genomes]
rs7162194	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7164655	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7169053	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7171073	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7171304	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7176873	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7178833	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8031516	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8031640	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8032615	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8033010	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8034066	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8035485	0.88[ASN][1000 genomes]
rs8039899	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8040708	0.94[EUR][1000 genomes]
rs9302200	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042486	chr15:57094598-57505992	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv542393	chr15:57115116-57341363	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv904250	chr15:57225766-57294085	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1052052	chr15:57232111-57344561	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv542394	chr15:57232111-57344561	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv904251	chr15:57241970-57575916	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8023816	LOC283663	Cis_1M	lymphoblastoid	RTeQTL
rs8023816	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57269800-57304800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:57273000-57307200	Weak transcription	Fetal Intestine Small	intestine
3	chr15:57274200-57289200	Weak transcription	Fetal Muscle Leg	muscle
4	chr15:57274200-57295600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr15:57275400-57306200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr15:57276200-57289200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr15:57276200-57313400	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr15:57277000-57313400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:57278600-57295400	Weak transcription	NH-A	brain
10	chr15:57279400-57300000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr15:57279600-57301800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr15:57279800-57300200	Weak transcription	Psoas Muscle	Psoas
13	chr15:57280600-57294000	Weak transcription	HSMMtube	muscle
14	chr15:57282000-57289200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr15:57282000-57289800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr15:57282000-57295400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr15:57282000-57295400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr15:57282000-57295600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr15:57282000-57307400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr15:57282000-57315000	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr15:57282200-57291800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr15:57282200-57295000	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr15:57282200-57295200	Weak transcription	Hela-S3	cervix
24	chr15:57282200-57295200	Weak transcription	NHLF	lung
25	chr15:57282200-57295600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr15:57282200-57295800	Weak transcription	Fetal Kidney	kidney
27	chr15:57282200-57298600	Weak transcription	Ovary	ovary
28	chr15:57282200-57299400	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr15:57282200-57308400	Weak transcription	Thymus	Thymus
30	chr15:57282200-57311000	Weak transcription	K562	blood
31	chr15:57282200-57315200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr15:57282600-57289800	Strong transcription	Fetal Thymus	thymus
33	chr15:57282600-57293800	Weak transcription	Fetal Heart	heart
34	chr15:57282600-57306200	Weak transcription	HepG2	liver
35	chr15:57283400-57291800	Weak transcription	Left Ventricle	heart
36	chr15:57283400-57291800	Weak transcription	Right Atrium	heart
37	chr15:57283800-57296400	Weak transcription	Fetal Stomach	stomach
38	chr15:57284200-57310800	Weak transcription	Fetal Muscle Trunk	muscle
39	chr15:57285800-57289000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr15:57286000-57289200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr15:57286000-57290400	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr15:57286000-57295200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr15:57286000-57295400	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr15:57286000-57296400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr15:57286000-57299400	Weak transcription	Primary T cells from cord blood	blood
46	chr15:57286000-57299800	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr15:57286000-57306200	Weak transcription	Fetal Intestine Large	intestine
48	chr15:57286000-57307400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr15:57286200-57288800	Weak transcription	Primary B cells from cord blood	blood
50	chr15:57286200-57289200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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