Variant report

Variant	rs3742354
Chromosome Location	chr14:39531281-39531282
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10133797	0.93[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap]
rs10134654	0.85[CEU][hapmap]
rs10136536	0.93[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10137988	1.00[ASW][hapmap];0.85[CEU][hapmap];0.87[CHD][hapmap];0.89[MEX][hapmap]
rs10140341	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10141471	0.90[ASN][1000 genomes]
rs10151683	0.91[CHB][hapmap]
rs1061583	1.00[ASW][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap]
rs11157041	0.94[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12147991	1.00[ASW][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap]
rs12164875	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12437031	0.85[CEU][hapmap]
rs12879229	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12883061	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12885242	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.89[AFR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12890771	1.00[ASW][hapmap];0.85[CEU][hapmap];0.87[CHD][hapmap];0.89[MEX][hapmap]
rs12894046	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1555257	0.81[CHB][hapmap];0.94[CHD][hapmap];0.91[ASN][1000 genomes]
rs17108728	0.90[ASN][1000 genomes]
rs17108846	1.00[ASW][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap]
rs2415524	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2737721	0.93[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap]
rs2737729	0.93[CHB][hapmap]
rs2753606	0.93[CHB][hapmap]
rs28485301	0.80[AMR][1000 genomes]
rs28502115	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2869	0.93[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap]
rs28699217	0.94[ASN][1000 genomes]
rs28810420	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34642409	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34676226	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34816815	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34985331	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35035794	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35224434	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35423721	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35992529	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36161173	0.93[ASN][1000 genomes]
rs3742355	0.94[ASN][1000 genomes]
rs3759545	0.93[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4143954	0.93[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.85[TSI][hapmap]
rs4902259	0.80[CEU][hapmap];0.84[CHD][hapmap];0.89[MEX][hapmap]
rs4902308	0.94[ASN][1000 genomes]
rs4902405	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4902406	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4902418	1.00[ASW][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap]
rs4902431	0.93[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap]
rs4902448	0.93[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap]
rs6571893	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71407775	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7147194	0.93[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.92[TSI][hapmap]
rs7152746	0.95[CEU][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs7153124	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9322992	0.95[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][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	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	nsv1038622	chr14:39423562-39604035	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv564417	chr14:39452317-39535560	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3742354	SIP1	Cis_1M	lymphoblastoid	RTeQTL
rs3742354	TRAPPC6B	cis	multi-tissue	Pritchard
rs3742354	MIA2	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39521200-39535600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr14:39523800-39540200	Weak transcription	Psoas Muscle	Psoas
3	chr14:39525400-39540600	Strong transcription	NH-A	brain
4	chr14:39525600-39533400	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr14:39525600-39533400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr14:39525600-39540600	Strong transcription	HSMM	muscle
7	chr14:39525600-39541000	Weak transcription	Brain Angular Gyrus	brain
8	chr14:39525600-39565600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr14:39526000-39537400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr14:39526000-39557200	Strong transcription	Osteobl	bone
11	chr14:39526200-39535200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr14:39526400-39563200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr14:39526600-39534200	Strong transcription	Brain Germinal Matrix	brain
14	chr14:39526800-39533400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr14:39526800-39534000	Weak transcription	Small Intestine	intestine
16	chr14:39526800-39534800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr14:39526800-39535000	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr14:39526800-39535400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr14:39526800-39535400	Strong transcription	NHDF-Ad	bronchial
20	chr14:39526800-39537200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr14:39526800-39538400	Strong transcription	Liver	Liver
22	chr14:39526800-39540400	Weak transcription	Spleen	Spleen
23	chr14:39526800-39540800	Weak transcription	Right Ventricle	heart
24	chr14:39526800-39541200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr14:39526800-39552600	Weak transcription	Gastric	stomach
26	chr14:39526800-39553800	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr14:39526800-39554000	Weak transcription	Aorta	Aorta
28	chr14:39526800-39554000	Weak transcription	Esophagus	oesophagus
29	chr14:39526800-39554200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr14:39526800-39554200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr14:39526800-39566600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr14:39527000-39532800	Weak transcription	Fetal Stomach	stomach
33	chr14:39527000-39536600	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr14:39527000-39537200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr14:39527000-39537200	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr14:39527000-39539000	Weak transcription	Lung	lung
37	chr14:39527000-39540600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr14:39527000-39540600	Weak transcription	Thymus	Thymus
39	chr14:39527000-39541800	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr14:39527000-39554200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr14:39527000-39565400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr14:39527400-39533400	Weak transcription	Fetal Brain Female	brain
43	chr14:39527400-39533400	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr14:39527400-39536000	Strong transcription	Fetal Lung	lung
45	chr14:39527400-39536400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr14:39527400-39536600	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr14:39527400-39536600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr14:39527400-39537200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr14:39527400-39538200	Strong transcription	Duodenum Mucosa	Duodenum
50	chr14:39527400-39538400	Strong transcription	HepG2	liver

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