Variant report

Variant	rs2733334
Chromosome Location	chr15:57439750-57439751
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:57428236..57433536-chr15:57434011..57440588,9	K562	blood:
2	chr15:57209403..57213183-chr15:57438186..57441495,3	MCF-7	breast:
3	chr15:57438759..57439994-chr15:57819455..57820425,3	K562	blood:
4	chr15:57438911..57440950-chr15:57443234..57446216,2	K562	blood:
5	chr15:57326879..57327856-chr15:57438827..57439782,2	K562	blood:

Variant related genes	Relation type
ENSG00000140262	Chromatin interaction
ENSG00000137871	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10467927	0.83[CHB][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes]
rs10467928	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs10467929	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs11071308	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11853810	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11856210	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11856411	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs12101455	0.85[EUR][1000 genomes]
rs12591430	0.87[EUR][1000 genomes]
rs13379847	0.86[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1430820	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs1430822	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs16977243	0.82[EUR][1000 genomes]
rs16977270	0.87[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes]
rs16977278	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs16977306	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs16977374	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs17415731	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs1841696	0.82[EUR][1000 genomes]
rs1841697	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2169467	0.83[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes]
rs2414493	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2591068	0.89[CEU][hapmap]
rs2593211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2593249	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2593250	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2593252	0.83[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes]
rs2615227	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2703593	0.88[CEU][hapmap]
rs2703595	0.94[CEU][hapmap]
rs2703614	0.83[CHB][hapmap];0.91[JPT][hapmap];0.84[EUR][1000 genomes]
rs2733310	0.88[CEU][hapmap]
rs2733323	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs2733333	0.83[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28372003	0.82[EUR][1000 genomes]
rs28536671	0.86[EUR][1000 genomes]
rs28712697	0.82[EUR][1000 genomes]
rs3803453	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs58479554	0.85[EUR][1000 genomes]
rs6493900	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs67077316	0.85[EUR][1000 genomes]
rs7162194	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7163126	0.86[EUR][1000 genomes]
rs7163267	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs7164298	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7169508	0.86[EUR][1000 genomes]
rs7171073	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs7173748	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs7176873	0.90[JPT][hapmap]
rs7178833	0.83[CHB][hapmap];0.85[JPT][hapmap]
rs7179311	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs7180558	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7181399	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs720290	0.84[CHB][hapmap]
rs8024901	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs8026702	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8031640	0.91[JPT][hapmap]
rs8032615	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs8034066	0.87[CHB][hapmap];0.83[JPT][hapmap]
rs8034502	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8034744	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs8034843	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs8035916	0.90[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8037956	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs8039176	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs8039899	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs9672676	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs9806170	0.83[CHB][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs9806199	0.83[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs997683	0.95[CHB][hapmap];1.00[JPT][hapmap]

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
rs2733334	LOC283663	Cis_1M	lymphoblastoid	RTeQTL
rs2733334	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57387600-57442400	Weak transcription	Fetal Intestine Large	intestine
2	chr15:57410600-57440800	Weak transcription	Ovary	ovary
3	chr15:57425800-57440800	Weak transcription	Thymus	Thymus
4	chr15:57425800-57442200	Weak transcription	Right Ventricle	heart
5	chr15:57427200-57440000	Weak transcription	Fetal Stomach	stomach
6	chr15:57427400-57442600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr15:57427600-57440600	Weak transcription	Dnd41	blood
8	chr15:57428400-57442200	Weak transcription	Primary T cells from cord blood	blood
9	chr15:57428600-57444000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr15:57433000-57444000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr15:57436000-57442200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr15:57436600-57440600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr15:57437000-57441000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr15:57437200-57440000	Weak transcription	Left Ventricle	heart
15	chr15:57437200-57441400	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr15:57437200-57442600	Weak transcription	K562	blood
17	chr15:57437800-57442000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr15:57438200-57440000	Weak transcription	Fetal Thymus	thymus
19	chr15:57438400-57442800	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr15:57438600-57444000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr15:57438800-57440400	Enhancers	Primary B cells from cord blood	blood
22	chr15:57438800-57440400	Enhancers	Duodenum Mucosa	Duodenum
23	chr15:57438800-57440800	Enhancers	GM12878-XiMat	blood
24	chr15:57438800-57441600	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr15:57438800-57441600	Enhancers	Liver	Liver
26	chr15:57439000-57441200	Weak transcription	NHEK	skin
27	chr15:57439000-57442800	Enhancers	Brain Substantia Nigra	brain
28	chr15:57439000-57463400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr15:57439200-57440000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr15:57439200-57440000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr15:57439200-57440000	Enhancers	Fetal Kidney	kidney
32	chr15:57439200-57440000	Weak transcription	Fetal Muscle Leg	muscle
33	chr15:57439200-57440000	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr15:57439200-57440200	Weak transcription	Aorta	Aorta
35	chr15:57439200-57440600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr15:57439200-57440800	Weak transcription	Stomach Smooth Muscle	stomach
37	chr15:57439200-57441000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr15:57439200-57441000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr15:57439200-57441000	Weak transcription	HMEC	breast
40	chr15:57439200-57441600	Enhancers	Brain Germinal Matrix	brain
41	chr15:57439200-57441600	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr15:57439200-57441600	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr15:57439200-57441600	Enhancers	Fetal Brain Male	brain
44	chr15:57439200-57441600	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr15:57439200-57442200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr15:57439200-57442400	Enhancers	Brain Cingulate Gyrus	brain
47	chr15:57439200-57442400	Enhancers	Colon Smooth Muscle	Colon
48	chr15:57439200-57442600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr15:57439200-57442800	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr15:57439200-57442800	Enhancers	Brain Angular Gyrus	brain

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