Variant report

Variant	rs28653088
Chromosome Location	chr15:57542893-57542894
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57539799..57542087-chr15:57542689..57545478,3	K562	blood:
2	chr15:57508073..57512585-chr15:57540435..57543693,4	K562	blood:

Variant related genes	Relation type
ENSG00000260689	Chromatin interaction
ENSG00000140262	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11853810	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11856210	0.85[ASN][1000 genomes]
rs16977278	0.81[ASN][1000 genomes]
rs16977374	0.93[ASN][1000 genomes]
rs2615226	0.99[ASN][1000 genomes]
rs2615227	0.99[ASN][1000 genomes]
rs2733323	0.82[ASN][1000 genomes]
rs28445470	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3803453	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4774915	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4774916	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55742030	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6493907	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7164298	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7164914	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7173477	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7173748	0.81[ASN][1000 genomes]
rs7180558	0.97[ASN][1000 genomes]
rs7181399	0.81[EUR][1000 genomes]
rs8024901	0.94[ASN][1000 genomes]
rs8026702	0.84[ASN][1000 genomes]
rs8034744	0.81[EUR][1000 genomes]
rs8034843	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8037956	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs8039176	0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs997683	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	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
2	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv457164	chr15:57495060-57559387	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv569578	chr15:57495060-57559387	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv833021	chr15:57495413-57751366	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28653088	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57511800-57551600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:57511800-57565000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr15:57519600-57544600	Weak transcription	Psoas Muscle	Psoas
4	chr15:57520400-57576000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr15:57520800-57544600	Weak transcription	Colon Smooth Muscle	Colon
6	chr15:57522400-57565400	Weak transcription	Spleen	Spleen
7	chr15:57522800-57585000	Strong transcription	Fetal Thymus	thymus
8	chr15:57525600-57556800	Weak transcription	Pancreas	Pancrea
9	chr15:57526000-57550200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr15:57526600-57545400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr15:57526600-57554400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr15:57526600-57574200	Weak transcription	Hela-S3	cervix
13	chr15:57526800-57545400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr15:57526800-57554200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr15:57528200-57545200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr15:57528400-57545400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr15:57528400-57554800	Weak transcription	NHEK	skin
18	chr15:57529000-57545400	Weak transcription	HMEC	breast
19	chr15:57529400-57543400	Weak transcription	HUVEC	blood vessel
20	chr15:57530200-57543400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr15:57530800-57551200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:57533600-57568800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr15:57536800-57574200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr15:57537000-57549200	Strong transcription	Dnd41	blood
25	chr15:57537800-57545400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr15:57537800-57551600	Weak transcription	Brain Germinal Matrix	brain
27	chr15:57537800-57551800	Weak transcription	Small Intestine	intestine
28	chr15:57537800-57555200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:57537800-57598200	Weak transcription	Colonic Mucosa	Colon
30	chr15:57538000-57543400	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr15:57538000-57543400	Weak transcription	NHDF-Ad	bronchial
32	chr15:57538400-57543600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr15:57538400-57551800	Weak transcription	Stomach Mucosa	stomach
34	chr15:57538400-57564800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr15:57538600-57543800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr15:57538600-57544000	Strong transcription	Fetal Kidney	kidney
37	chr15:57538600-57551800	Weak transcription	Brain Cingulate Gyrus	brain
38	chr15:57538800-57543400	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr15:57538800-57554200	Weak transcription	Fetal Brain Female	brain
40	chr15:57539200-57543200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr15:57539200-57543400	Weak transcription	Brain Substantia Nigra	brain
42	chr15:57539200-57543600	Weak transcription	Brain Angular Gyrus	brain
43	chr15:57539400-57554400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr15:57539400-57574800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr15:57539600-57543200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr15:57539600-57543400	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr15:57539600-57543400	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr15:57539600-57543600	Weak transcription	Brain Hippocampus Middle	brain
49	chr15:57539600-57544200	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr15:57539600-57544600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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