Variant report

Variant	rs12437405
Chromosome Location	chr14:39618412-39618413
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:39615859..39619392-chr14:39639334..39641256,3	MCF-7	breast:
2	chr14:39614473..39616269-chr14:39616886..39619440,2	MCF-7	breast:
3	chr14:39616786..39619391-chr14:39641245..39644143,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182400	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10130972	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10133797	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10136536	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10149120	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10151683	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12147991	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12891258	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12894046	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12895751	0.81[EUR][1000 genomes]
rs13379360	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17108846	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2737721	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2737729	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2753606	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28379470	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28485301	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2869	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28856917	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34816815	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35035794	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3759545	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4143954	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4902405	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4902406	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4902418	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902435	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902448	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs532	0.81[EUR][1000 genomes]
rs57653321	0.84[AFR][1000 genomes]
rs58851254	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67248626	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71407780	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7147194	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7153124	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs73291544	0.84[AFR][1000 genomes]
rs8006879	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9322994	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3429206	chr14:39160730-39648836	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1051247	chr14:39604035-39652789	Genic enhancers Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12437405	TRAPPC6B	cis	multi-tissue	Pritchard
rs12437405	SIP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39583800-39626000	Weak transcription	Spleen	Spleen
2	chr14:39584000-39623600	Weak transcription	Esophagus	oesophagus
3	chr14:39584200-39636000	Weak transcription	Small Intestine	intestine
4	chr14:39584200-39638600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr14:39584400-39620800	Weak transcription	Colonic Mucosa	Colon
6	chr14:39584400-39626600	Weak transcription	Aorta	Aorta
7	chr14:39584600-39625800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr14:39588600-39635400	Weak transcription	Fetal Brain Male	brain
9	chr14:39589200-39626400	Weak transcription	Fetal Heart	heart
10	chr14:39592600-39622200	Weak transcription	Right Ventricle	heart
11	chr14:39592800-39626600	Weak transcription	NHLF	lung
12	chr14:39594000-39620800	Weak transcription	Hela-S3	cervix
13	chr14:39596200-39621200	Weak transcription	Brain Substantia Nigra	brain
14	chr14:39598800-39636200	Weak transcription	Stomach Mucosa	stomach
15	chr14:39604400-39635400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr14:39604800-39622400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr14:39605200-39621200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr14:39605800-39625200	Weak transcription	HSMMtube	muscle
19	chr14:39606800-39621200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr14:39607000-39621200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr14:39607000-39625400	Weak transcription	Fetal Kidney	kidney
22	chr14:39607200-39619400	Weak transcription	HMEC	breast
23	chr14:39607200-39623800	Weak transcription	Ovary	ovary
24	chr14:39608200-39620000	Weak transcription	Brain Angular Gyrus	brain
25	chr14:39608200-39622000	Weak transcription	Brain Anterior Caudate	brain
26	chr14:39608200-39630600	Weak transcription	NHEK	skin
27	chr14:39608800-39620000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr14:39610000-39623000	Weak transcription	Gastric	stomach
29	chr14:39611000-39619800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr14:39611000-39619800	Weak transcription	Lung	lung
31	chr14:39611000-39622000	Weak transcription	Thymus	Thymus
32	chr14:39611000-39622200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr14:39611000-39637600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr14:39611200-39619800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr14:39611200-39621000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr14:39611200-39621000	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr14:39611200-39622400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr14:39611200-39622600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr14:39611200-39638800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr14:39611400-39618600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr14:39611400-39619800	Weak transcription	Fetal Intestine Small	intestine
42	chr14:39611400-39622600	Weak transcription	Brain Germinal Matrix	brain
43	chr14:39611400-39638000	Weak transcription	A549	lung
44	chr14:39612000-39631600	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr14:39612400-39619600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr14:39612400-39625400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr14:39612800-39637800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr14:39614200-39628200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr14:39614400-39636800	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr14:39614800-39636800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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