Variant report

Variant	rs28781690
Chromosome Location	chr15:57466974-57466975
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10467927	0.83[EUR][1000 genomes]
rs10467928	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10467929	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11071308	0.82[EUR][1000 genomes]
rs11856210	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12101455	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12591430	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13379847	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16977243	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16977270	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16977278	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16977306	0.86[EUR][1000 genomes]
rs1841697	0.81[EUR][1000 genomes]
rs2169467	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2414493	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2593252	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2703614	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2733333	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28372003	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28536671	0.86[EUR][1000 genomes]
rs28712697	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58479554	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6493900	0.83[AMR][1000 genomes]
rs67077316	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7163126	0.86[EUR][1000 genomes]
rs7163267	0.81[AMR][1000 genomes]
rs7169508	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7173748	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7179311	0.85[EUR][1000 genomes]
rs7181399	0.84[EUR][1000 genomes]
rs720290	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8023736	0.83[AMR][1000 genomes]
rs8026702	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8034744	0.84[EUR][1000 genomes]
rs8035916	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9672676	0.86[EUR][1000 genomes]
rs9806170	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9806199	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
3	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28781690	TCF12	Cis_1M	lymphoblastoid	RTeQTL
rs28781690	LOC283663	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57439400-57491600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr15:57444400-57485600	Weak transcription	Placenta	Placenta
3	chr15:57444400-57507400	Weak transcription	K562	blood
4	chr15:57444600-57490200	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr15:57444800-57484200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:57444800-57484200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr15:57445400-57478400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr15:57446000-57468400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr15:57447000-57484600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr15:57448000-57483800	Weak transcription	Lung	lung
11	chr15:57450800-57469000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr15:57450800-57491000	Weak transcription	Left Ventricle	heart
13	chr15:57451000-57477400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr15:57451000-57487800	Weak transcription	Psoas Muscle	Psoas
15	chr15:57451000-57490800	Weak transcription	NHEK	skin
16	chr15:57451200-57470200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr15:57451200-57475000	Weak transcription	Colon Smooth Muscle	Colon
18	chr15:57451200-57475400	Weak transcription	Adipose Nuclei	Adipose
19	chr15:57451200-57478600	Weak transcription	HMEC	breast
20	chr15:57451200-57484200	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr15:57451200-57484200	Weak transcription	Esophagus	oesophagus
22	chr15:57451200-57490400	Weak transcription	Ovary	ovary
23	chr15:57451600-57491200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr15:57451800-57478400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr15:57452200-57481600	Weak transcription	Fetal Heart	heart
26	chr15:57452400-57475400	Weak transcription	Fetal Lung	lung
27	chr15:57452400-57490400	Weak transcription	Fetal Brain Female	brain
28	chr15:57452800-57470800	Weak transcription	Brain Anterior Caudate	brain
29	chr15:57453800-57485400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr15:57453800-57524600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr15:57457200-57499400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr15:57457400-57478400	Weak transcription	Fetal Muscle Leg	muscle
33	chr15:57458200-57505200	Strong transcription	Fetal Thymus	thymus
34	chr15:57458600-57468600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr15:57458800-57475000	Weak transcription	Osteobl	bone
36	chr15:57458800-57475600	Weak transcription	HUVEC	blood vessel
37	chr15:57459200-57488600	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr15:57459200-57492600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr15:57459400-57468600	Weak transcription	HSMM	muscle
40	chr15:57459600-57469000	Weak transcription	Primary hematopoietic stem cells	blood
41	chr15:57459800-57475600	Weak transcription	Fetal Intestine Large	intestine
42	chr15:57459800-57476200	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr15:57459800-57476600	Weak transcription	Fetal Stomach	stomach
44	chr15:57459800-57477400	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr15:57459800-57477800	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr15:57459800-57478400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr15:57459800-57490200	Weak transcription	HSMMtube	muscle
48	chr15:57460000-57484200	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr15:57460400-57468200	Weak transcription	Thymus	Thymus
50	chr15:57460400-57468600	Weak transcription	Primary B cells from cord blood	blood

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