Variant report

Variant	rs10149249
Chromosome Location	chr14:104047757-104047758
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:104047041..104049916-chr14:104095707..104097301,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BAG5-1	chr14:104047007-104049243	ucscGeneNc_uc001you_1

Extended variants
information (count: 46 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10134399	0.96[CEU][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes]
rs10135248	0.88[CEU][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.89[TSI][hapmap]
rs10140410	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10143293	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11621777	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11622552	0.83[JPT][hapmap]
rs11626658	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11626905	0.84[JPT][hapmap]
rs2274268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2274269	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2403205	0.91[ASW][hapmap];0.88[CEU][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.84[LWK][hapmap];0.91[TSI][hapmap]
rs28513222	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28514618	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28660416	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28744517	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3783404	0.88[CEU][hapmap];0.91[JPT][hapmap]
rs55864158	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56017123	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57447494	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59281218	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60802358	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61996716	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61996717	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61996718	0.89[ASN][1000 genomes]
rs61996721	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs709400	0.91[ASW][hapmap];0.88[CEU][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap];0.91[TSI][hapmap]
rs7142883	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7150141	0.88[CEU][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.89[TSI][hapmap]
rs7154587	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7154948	0.82[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7693	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs861528	0.91[JPT][hapmap]
rs861531	0.88[CEU][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.89[TSI][hapmap]
rs861534	0.86[CEU][hapmap];0.81[JPT][hapmap]
rs861536	0.91[ASW][hapmap];0.88[CEU][hapmap];0.84[GIH][hapmap];0.83[LWK][hapmap];0.89[TSI][hapmap]
rs861539	0.91[ASW][hapmap];0.84[CEU][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.84[LWK][hapmap];0.87[TSI][hapmap]
rs942863	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv902297	chr14:103956182-104061646	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv902298	chr14:103959289-104061646	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv902299	chr14:103967504-104061646	Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv902300	chr14:103967504-104205811	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
7	nsv902304	chr14:103979953-104061646	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
8	nsv902305	chr14:103979953-104073551	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
9	nsv566022	chr14:104007555-104092789	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10149249	APOPT1	cis	Muscle Skeletal	GTEx
rs10149249	KLC1	cis	parietal	SCAN
rs10149249	BAG5	cis	multi-tissue	Pritchard
rs10149249	BAG5	cis	cerebellum	SCAN
rs10149249	C14orf153	cis	cerebellum	SCAN
rs10149249	DNAH8	trans	parietal	SCAN
rs10149249	C14orf153	cis	parietal	SCAN
rs10149249	ZFYVE21	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104030800-104073200	Weak transcription	Small Intestine	intestine
2	chr14:104035400-104060400	Weak transcription	Fetal Brain Male	brain
3	chr14:104037400-104048400	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr14:104038400-104048800	Strong transcription	Fetal Brain Female	brain
5	chr14:104038400-104049400	Strong transcription	Primary T cells from cord blood	blood
6	chr14:104038800-104051000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr14:104041000-104059600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr14:104041000-104063200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr14:104041600-104056200	Weak transcription	K562	blood
10	chr14:104041600-104056400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr14:104041800-104052600	Weak transcription	Psoas Muscle	Psoas
12	chr14:104041800-104059600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr14:104041800-104060600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr14:104042200-104057200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr14:104043400-104049200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr14:104043400-104051200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr14:104043400-104051200	Strong transcription	Fetal Intestine Large	intestine
18	chr14:104043400-104052000	Strong transcription	Fetal Intestine Small	intestine
19	chr14:104043400-104056600	Weak transcription	Fetal Heart	heart
20	chr14:104043600-104048000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr14:104043600-104048400	Strong transcription	HSMM	muscle
22	chr14:104043800-104049200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr14:104043800-104050800	Strong transcription	Fetal Muscle Trunk	muscle
24	chr14:104043800-104051400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr14:104043800-104051600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr14:104043800-104051600	Strong transcription	Fetal Muscle Leg	muscle
27	chr14:104043800-104055400	Weak transcription	Brain Angular Gyrus	brain
28	chr14:104043800-104058200	Strong transcription	Fetal Stomach	stomach
29	chr14:104043800-104059600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr14:104043800-104060200	Weak transcription	Stomach Mucosa	stomach
31	chr14:104044000-104048000	Weak transcription	NHEK	skin
32	chr14:104044000-104049000	Strong transcription	Brain Germinal Matrix	brain
33	chr14:104044000-104055000	Weak transcription	Colon Smooth Muscle	Colon
34	chr14:104044000-104056600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr14:104044400-104048200	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr14:104044600-104048800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr14:104044600-104049000	Strong transcription	Adipose Nuclei	Adipose
38	chr14:104044600-104049200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr14:104044600-104051000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr14:104045000-104048400	Strong transcription	Liver	Liver
41	chr14:104045000-104049000	Strong transcription	Pancreas	Pancrea
42	chr14:104045200-104048800	Strong transcription	Lung	lung
43	chr14:104045200-104049200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr14:104045200-104050000	Weak transcription	HSMMtube	muscle
45	chr14:104045200-104059600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr14:104045400-104048600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr14:104045400-104049000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr14:104045400-104050800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr14:104045400-104054600	Weak transcription	Ovary	ovary
50	chr14:104045400-104055200	Weak transcription	A549	lung

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