Variant report

Variant	rs12879085
Chromosome Location	chr14:103874420-103874421
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	chr14:103799851..103802065-chr14:103872940..103875846,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100664	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10133035	0.81[EUR][1000 genomes]
rs10134580	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1013650	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10139279	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10141120	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10141388	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10141433	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10143247	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10145793	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10150072	0.84[EUR][1000 genomes]
rs1028613	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11621037	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11621510	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11622356	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11622835	0.93[JPT][hapmap]
rs11623869	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11624367	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11626483	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11626905	0.86[JPT][hapmap]
rs11627052	0.83[CHD][hapmap];0.93[JPT][hapmap]
rs11628213	0.88[EUR][1000 genomes]
rs11628969	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12888077	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12889639	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12890750	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12898029	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1467561	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap]
rs17617941	0.88[EUR][1000 genomes]
rs17679475	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1803283	0.96[CEU][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs1951392	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1961600	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1989565	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2010281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2273699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs2273700	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2273703	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2296484	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap]
rs2403180	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28361338	0.81[EUR][1000 genomes]
rs28369539	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28444993	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28496120	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28583452	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28626081	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34216351	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3742458	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3759579	0.88[CEU][hapmap];0.85[TSI][hapmap];0.81[ASN][1000 genomes]
rs3783394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3783395	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3783402	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs3825566	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4243738	0.81[AFR][1000 genomes]
rs4243739	0.81[AFR][1000 genomes]
rs4900572	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4906319	0.82[YRI][hapmap]
rs4906320	0.82[YRI][hapmap]
rs4906321	0.96[CEU][hapmap];0.86[GIH][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs55859054	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56365443	0.88[EUR][1000 genomes]
rs62006268	0.88[EUR][1000 genomes]
rs62007681	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62007683	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62007684	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62007686	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62007687	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62007718	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62007719	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6575983	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6575984	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7140564	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7140647	0.81[YRI][hapmap]
rs71419613	0.82[AMR][1000 genomes]
rs7145113	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7146506	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7149767	0.86[YRI][hapmap]
rs7150317	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7152202	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7154246	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7155014	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7156150	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7156619	0.82[AMR][1000 genomes]
rs7158144	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7158822	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7160208	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7160366	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72708854	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72708874	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72708893	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8013101	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8015918	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[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]
rs8019578	0.84[EUR][1000 genomes]
rs9671911	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv9168	chr14:103531729-103913306	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12879085	BAG5	cis	multi-tissue	Pritchard
rs12879085	BAG5	Cis_1M	lymphoblastoid	RTeQTL
rs12879085	EIF5	cis	cerebellum	SCAN
rs12879085	MARK3	cis	Thyroid	GTEx
rs12879085	KLC1	cis	parietal	SCAN
rs12879085	MARK3	cis	cerebellum	SCAN
rs12879085	C14orf153	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:103855000-103874800	Weak transcription	Fetal Brain Male	brain
2	chr14:103861000-103874800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr14:103861000-103882400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr14:103862000-103919400	Weak transcription	Colonic Mucosa	Colon
5	chr14:103866600-103883400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr14:103868400-103878400	Weak transcription	Fetal Kidney	kidney
7	chr14:103868400-103880000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr14:103868400-103883200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr14:103868400-103883800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr14:103868600-103883200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr14:103869200-103878400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr14:103869600-103882800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr14:103870600-103878400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr14:103870800-103883200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr14:103870800-103883200	Weak transcription	HSMMtube	muscle
16	chr14:103871000-103874800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr14:103871000-103874800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr14:103871000-103874800	Weak transcription	Colon Smooth Muscle	Colon
19	chr14:103871000-103875200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr14:103871000-103875200	Strong transcription	GM12878-XiMat	blood
21	chr14:103871000-103875400	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr14:103871000-103878000	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr14:103871000-103878600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr14:103871000-103883000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr14:103871000-103883200	Weak transcription	Aorta	Aorta
26	chr14:103871000-103883600	Strong transcription	Dnd41	blood
27	chr14:103871000-103884400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr14:103871200-103874800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr14:103871200-103874800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr14:103871200-103874800	Weak transcription	Brain Substantia Nigra	brain
31	chr14:103871200-103875000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr14:103871200-103878400	Weak transcription	Esophagus	oesophagus
33	chr14:103871200-103878600	Weak transcription	NHLF	lung
34	chr14:103871200-103880000	Weak transcription	NHDF-Ad	bronchial
35	chr14:103871400-103874800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr14:103871400-103874800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr14:103871400-103874800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr14:103871400-103874800	Strong transcription	Fetal Intestine Small	intestine
39	chr14:103871400-103874800	Strong transcription	NHEK	skin
40	chr14:103871400-103875000	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr14:103871400-103875200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr14:103871400-103875200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr14:103871400-103875400	Strong transcription	Fetal Intestine Large	intestine
44	chr14:103871400-103875400	Strong transcription	Fetal Muscle Trunk	muscle
45	chr14:103871400-103875400	Strong transcription	Fetal Muscle Leg	muscle
46	chr14:103871400-103875400	Strong transcription	Fetal Thymus	thymus
47	chr14:103871400-103875600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr14:103871400-103878000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr14:103871400-103879600	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr14:103871400-103881200	Strong transcription	Monocytes-CD14+_RO01746	blood

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