Variant report

Variant	rs11853810
Chromosome Location	chr15:57545292-57545293
allele	A/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:

Variant related genes	Relation type
ENSG00000260689	Chromatin interaction
ENSG00000140262	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10467927	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs10467928	0.91[JPT][hapmap]
rs10467929	0.91[JPT][hapmap]
rs11071308	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11856210	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11856411	0.86[JPT][hapmap]
rs13379847	0.80[CHB][hapmap];0.91[JPT][hapmap]
rs16977270	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs16977278	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[ASN][1000 genomes]
rs16977306	0.83[CEU][hapmap]
rs16977374	0.82[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs2169467	0.91[JPT][hapmap]
rs2414493	0.81[JPT][hapmap]
rs2593211	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2593249	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2593252	0.90[JPT][hapmap]
rs2615226	0.97[ASN][1000 genomes]
rs2615227	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.99[ASN][1000 genomes]
rs2703593	0.82[CEU][hapmap]
rs2703614	0.91[JPT][hapmap]
rs2733310	0.82[CEU][hapmap]
rs2733323	0.88[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2733333	0.91[JPT][hapmap]
rs2733334	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs28445470	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28653088	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3803453	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4774915	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4774916	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55742030	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6493900	0.91[JPT][hapmap]
rs6493907	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7163267	0.91[JPT][hapmap]
rs7164298	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7164914	0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7171073	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7173477	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7173748	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[ASN][1000 genomes]
rs7176873	0.90[JPT][hapmap]
rs7179311	0.88[CEU][hapmap]
rs7180558	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs7181399	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs8024901	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs8026702	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs8031866	0.82[YRI][hapmap]
rs8034502	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs8034744	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs8034843	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8035916	0.90[JPT][hapmap]
rs8037901	0.85[YRI][hapmap]
rs8037956	0.80[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.92[ASN][1000 genomes]
rs8039176	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.92[ASN][1000 genomes]
rs9672676	0.88[CEU][hapmap]
rs9806170	0.81[JPT][hapmap]
rs9806199	0.91[JPT][hapmap]
rs997683	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[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
rs11853810	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 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	chr15:57520400-57576000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr15:57522400-57565400	Weak transcription	Spleen	Spleen
5	chr15:57522800-57585000	Strong transcription	Fetal Thymus	thymus
6	chr15:57525600-57556800	Weak transcription	Pancreas	Pancrea
7	chr15:57526000-57550200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:57526600-57545400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr15:57526600-57554400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr15:57526600-57574200	Weak transcription	Hela-S3	cervix
11	chr15:57526800-57545400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr15:57526800-57554200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr15:57528400-57545400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr15:57528400-57554800	Weak transcription	NHEK	skin
15	chr15:57529000-57545400	Weak transcription	HMEC	breast
16	chr15:57530800-57551200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:57533600-57568800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr15:57536800-57574200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr15:57537000-57549200	Strong transcription	Dnd41	blood
20	chr15:57537800-57545400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr15:57537800-57551600	Weak transcription	Brain Germinal Matrix	brain
22	chr15:57537800-57551800	Weak transcription	Small Intestine	intestine
23	chr15:57537800-57555200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:57537800-57598200	Weak transcription	Colonic Mucosa	Colon
25	chr15:57538400-57551800	Weak transcription	Stomach Mucosa	stomach
26	chr15:57538400-57564800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr15:57538600-57551800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr15:57538800-57554200	Weak transcription	Fetal Brain Female	brain
29	chr15:57539400-57554400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr15:57539400-57574800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr15:57539600-57545400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr15:57539600-57545400	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr15:57539600-57551400	Weak transcription	Brain Anterior Caudate	brain
34	chr15:57539600-57556800	Weak transcription	Gastric	stomach
35	chr15:57539600-57565200	Weak transcription	Aorta	Aorta
36	chr15:57539600-57565200	Weak transcription	Esophagus	oesophagus
37	chr15:57540000-57545400	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr15:57540000-57545600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr15:57540000-57554400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr15:57540200-57545400	Weak transcription	Primary B cells from peripheral blood	blood
41	chr15:57540200-57547600	Weak transcription	Stomach Smooth Muscle	stomach
42	chr15:57540200-57551800	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr15:57540200-57555000	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr15:57540600-57545400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr15:57540600-57545400	Weak transcription	Placenta	Placenta
46	chr15:57540600-57545400	Weak transcription	Left Ventricle	heart
47	chr15:57540600-57551800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr15:57540600-57556800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr15:57540600-57557000	Weak transcription	Lung	lung
50	chr15:57540600-57565400	Weak transcription	Ovary	ovary

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