Variant report

Variant	rs3742458
Chromosome Location	chr14:103950368-103950369
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	chr14:103948825..103951654-chr14:103995758..103998626,2	K562	blood:

Extended variants
information (count: 109 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10133035	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10134580	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10135868	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1013650	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10139279	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10141120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10141388	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10141433	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10143247	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10144051	0.86[YRI][hapmap]
rs10145793	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10148970	0.90[YRI][hapmap]
rs10150072	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10162425	0.89[YRI][hapmap]
rs1022736	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1028613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11621037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs11621510	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11622356	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11622835	0.83[CHD][hapmap];0.93[JPT][hapmap]
rs11623470	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11623869	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11624367	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11626483	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11626787	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11626905	0.86[JPT][hapmap]
rs11627052	0.93[JPT][hapmap]
rs11627529	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11628213	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11628969	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12879085	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12888077	0.87[EUR][1000 genomes]
rs12889639	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12890750	0.87[EUR][1000 genomes]
rs12898029	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1467561	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17617941	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17679475	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1803283	1.00[CEU][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1951392	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1961600	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1989565	0.96[CEU][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2010281	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2273699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2273700	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2273703	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296484	1.00[CEU][hapmap];0.85[CHB][hapmap];0.80[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2296486	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2403180	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28361338	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28369539	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28444993	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28496120	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28583452	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28626081	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34216351	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3759579	0.84[CEU][hapmap];0.85[TSI][hapmap]
rs3759584	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3783394	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3783395	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3783402	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3825566	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4143998	0.83[YRI][hapmap]
rs45441198	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4900572	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4906321	0.91[CEU][hapmap];0.86[GIH][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs55723020	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55859054	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56365443	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62006268	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62007681	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62007683	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62007684	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62007686	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62007687	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62007718	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007719	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6575983	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6575984	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7140564	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7145113	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7146506	0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7148567	0.86[YRI][hapmap]
rs7150317	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7152202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7154246	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7155014	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7156150	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7158144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7158822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7160208	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7160366	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72708854	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72708874	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72708893	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72710714	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8013101	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8015918	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8019578	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9671414	0.86[YRI][hapmap]
rs9671911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049747	chr14:103126148-103955984	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
2	nsv534254	chr14:103470073-104023906	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
3	esv3332028	chr14:103581471-104328811	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
4	nsv832883	chr14:103927687-104120953	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
5	nsv525874	chr14:103937372-103950368	Genic enhancers Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv1829466	chr14:103937582-103954794	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv1835815	chr14:103942991-103989757	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	29 gene(s)	inside rSNPs	diseases
8	nsv85551	chr14:103948122-103951588	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3742458	BAG5	cis	multi-tissue	Pritchard
rs3742458	MARK3	cis	Thyroid	GTEx
rs3742458	KLC1	cis	parietal	SCAN
rs3742458	CKB	cis	Skin Sun Exposed Lower leg	GTEx
rs3742458	BAG5	Cis_1M	lymphoblastoid	RTeQTL
rs3742458	C14orf153	cis	cerebellum	SCAN
rs3742458	MARK3	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:103922400-103955000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr14:103923200-103976800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr14:103923600-103967000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr14:103924000-103957400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr14:103925600-103958400	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr14:103926200-103950400	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr14:103926800-103963400	Strong transcription	Fetal Intestine Large	intestine
8	chr14:103927800-103951000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr14:103927800-103951600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr14:103927800-103979800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr14:103928600-103950800	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr14:103930600-103951800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr14:103931600-103955000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr14:103932000-103953800	Strong transcription	Fetal Muscle Leg	muscle
15	chr14:103939200-103950800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr14:103939200-103951000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr14:103939200-103951000	Strong transcription	Liver	Liver
18	chr14:103939200-103951000	Strong transcription	Placenta	Placenta
19	chr14:103939200-103966200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr14:103939400-103950400	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr14:103939400-103950800	Strong transcription	Dnd41	blood
22	chr14:103939400-103952200	Strong transcription	Fetal Muscle Trunk	muscle
23	chr14:103939400-103956000	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr14:103940200-103954800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr14:103940400-103950400	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr14:103940400-103950800	Strong transcription	Adipose Nuclei	Adipose
27	chr14:103940400-103951000	Strong transcription	Brain Hippocampus Middle	brain
28	chr14:103941600-103953800	Weak transcription	Small Intestine	intestine
29	chr14:103942800-103956000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr14:103942800-103957200	Weak transcription	Brain Angular Gyrus	brain
31	chr14:103942800-103966400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr14:103943200-103969200	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr14:103943400-103953800	Weak transcription	Right Ventricle	heart
34	chr14:103943400-103954800	Weak transcription	Fetal Heart	heart
35	chr14:103943400-103958200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr14:103943600-103951800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr14:103943600-103953800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr14:103944200-103955600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr14:103944400-103953400	Weak transcription	Esophagus	oesophagus
40	chr14:103944400-103957400	Weak transcription	Colonic Mucosa	Colon
41	chr14:103944400-103962200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr14:103945000-103950400	Strong transcription	Brain Substantia Nigra	brain
43	chr14:103945200-103950800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr14:103945400-103962800	Strong transcription	Thymus	Thymus
45	chr14:103945600-103954200	Weak transcription	Fetal Brain Male	brain
46	chr14:103945600-103957400	Weak transcription	Brain Cingulate Gyrus	brain
47	chr14:103946400-103950400	Strong transcription	Hela-S3	cervix
48	chr14:103946400-103964400	Strong transcription	Fetal Thymus	thymus
49	chr14:103946600-103950400	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr14:103946600-103950600	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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