Variant report

Variant	rs2414493
Chromosome Location	chr15:57519518-57519519
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:57518271..57520593-chr15:57524473..57526151,2	K562	blood:
2	chr15:57514341..57517314-chr15:57518774..57520989,2	MCF-7	breast:
3	chr15:57516204..57519771-chr15:57520107..57524216,4	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10467927	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs10467928	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10467929	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11071308	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs11853810	0.81[JPT][hapmap]
rs11856210	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs11856411	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs13379847	0.90[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs16977243	0.91[CEU][hapmap];0.91[CHB][hapmap];0.92[YRI][hapmap]
rs16977270	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs16977278	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs2169467	0.83[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap]
rs2593211	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs2593249	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2593252	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs2615227	0.90[JPT][hapmap]
rs2703614	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2733333	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2733334	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs28781690	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3803453	0.85[JPT][hapmap]
rs6493900	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap]
rs7163267	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs7164298	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs7171073	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs7171304	0.88[CEU][hapmap]
rs7173748	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs7176873	0.84[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap]
rs7180558	0.82[CHB][hapmap]
rs7181399	0.80[EUR][1000 genomes]
rs720290	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8024901	0.85[JPT][hapmap]
rs8026702	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs8034502	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs8034744	0.80[EUR][1000 genomes]
rs8035916	0.84[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap]
rs8037956	0.81[CHB][hapmap];0.87[JPT][hapmap]
rs8039176	0.82[CHB][hapmap]
rs9302200	0.91[CEU][hapmap]
rs9806170	0.91[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap]
rs9806199	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs997683	0.81[JPT][hapmap]

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
rs2414493	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57453800-57524600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr15:57478800-57526200	Weak transcription	Hela-S3	cervix
3	chr15:57479400-57524800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:57481800-57524600	Weak transcription	Right Ventricle	heart
5	chr15:57487000-57524400	Weak transcription	Placenta	Placenta
6	chr15:57501200-57524400	Weak transcription	Thymus	Thymus
7	chr15:57507000-57519800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr15:57508200-57522800	Weak transcription	Fetal Thymus	thymus
9	chr15:57508600-57524400	Weak transcription	HepG2	liver
10	chr15:57509200-57526200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr15:57510600-57519800	Weak transcription	Dnd41	blood
12	chr15:57510600-57524400	Weak transcription	Liver	Liver
13	chr15:57510600-57524600	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr15:57511200-57525400	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr15:57511600-57525600	Weak transcription	A549	lung
16	chr15:57511600-57528000	Weak transcription	Fetal Heart	heart
17	chr15:57511800-57519600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr15:57511800-57520600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr15:57511800-57520800	Weak transcription	Small Intestine	intestine
20	chr15:57511800-57524400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr15:57511800-57524400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr15:57511800-57524400	Weak transcription	HMEC	breast
23	chr15:57511800-57524600	Weak transcription	Primary B cells from peripheral blood	blood
24	chr15:57511800-57524600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr15:57511800-57525800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr15:57511800-57528400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr15:57511800-57551600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr15:57511800-57565000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr15:57512000-57523400	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr15:57512000-57524600	Weak transcription	Primary B cells from cord blood	blood
31	chr15:57512000-57527200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr15:57512200-57524400	Weak transcription	Left Ventricle	heart
33	chr15:57512200-57524600	Weak transcription	Ovary	ovary
34	chr15:57512600-57524400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr15:57512600-57524400	Weak transcription	Fetal Intestine Large	intestine
36	chr15:57512800-57520400	Weak transcription	Adipose Nuclei	Adipose
37	chr15:57512800-57524400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr15:57513400-57519800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr15:57513600-57523800	Weak transcription	Stomach Smooth Muscle	stomach
40	chr15:57513800-57521200	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr15:57513800-57524400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr15:57513800-57524400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr15:57513800-57524400	Weak transcription	Fetal Muscle Trunk	muscle
44	chr15:57513800-57524400	Weak transcription	Fetal Stomach	stomach
45	chr15:57513800-57524600	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr15:57513800-57524600	Weak transcription	Fetal Brain Male	brain
47	chr15:57513800-57525400	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr15:57514000-57524600	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr15:57514200-57524600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr15:57514600-57524400	Weak transcription	Fetal Muscle Leg	muscle

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