Variant report

Variant	rs1028613
Chromosome Location	chr14:103888324-103888325
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:103874646..103876985-chr14:103887781..103889721,2	MCF-7	breast:
2	chr14:103799964..103801993-chr14:103887710..103889649,2	MCF-7	breast:
3	chr14:103878753..103883496-chr14:103884428..103888484,4	MCF-7	breast:
4	chr14:103887007..103890737-chr14:103900205..103902802,3	MCF-7	breast:
5	chr14:103885868..103889537-chr14:103891147..103894147,4	K562	blood:
6	chr14:103878188..103883188-chr14:103884541..103889590,5	MCF-7	breast:
7	chr14:103801788..103804728-chr14:103887482..103891031,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000244691	Chromatin interaction
ENSG00000272533	Chromatin interaction
ENSG00000100664	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10133035	0.81[EUR][1000 genomes]
rs10134580	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1013650	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10139279	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10141120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10141388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10141433	0.88[EUR][1000 genomes]
rs10143247	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10145793	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10150072	0.84[EUR][1000 genomes]
rs11621037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11621510	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11622356	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11622835	0.93[JPT][hapmap]
rs11623869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11624367	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11626483	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11626787	0.80[EUR][1000 genomes]
rs11626905	0.86[JPT][hapmap]
rs11627052	0.93[JPT][hapmap];1.00[YRI][hapmap]
rs11628213	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11628969	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12879085	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12888077	0.91[EUR][1000 genomes]
rs12889639	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12890750	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12898029	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1467561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17617941	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs17679475	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1803283	1.00[CEU][hapmap];0.87[JPT][hapmap]
rs1951392	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1961600	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1989565	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2010281	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2273699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2273700	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2273703	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2296484	1.00[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap]
rs2403180	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28361338	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28369539	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28444993	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28496120	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28583452	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28626081	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34216351	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3742458	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3759579	0.84[CEU][hapmap]
rs3783394	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3783395	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3783402	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs3825566	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4900572	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4906321	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs55723020	0.80[EUR][1000 genomes]
rs55859054	0.83[EUR][1000 genomes]
rs56365443	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs62006268	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs62007681	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62007683	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62007684	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62007686	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62007687	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62007718	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62007719	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6575983	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6575984	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7140564	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7145113	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7146506	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7150317	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7152202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7154246	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7155014	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7156150	0.86[EUR][1000 genomes]
rs7158144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7158822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7160208	0.87[EUR][1000 genomes]
rs7160366	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72708854	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72708874	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72708893	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72710714	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs8013101	0.88[EUR][1000 genomes]
rs8015918	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8019578	0.84[EUR][1000 genomes]
rs9671911	1.00[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1028613	BAG5	cis	multi-tissue	Pritchard
rs1028613	MARK3	cis	Thyroid	GTEx
rs1028613	BAG5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:103862000-103919400	Weak transcription	Colonic Mucosa	Colon
2	chr14:103874600-103900800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr14:103875200-103889200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr14:103875200-103893600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr14:103875400-103888600	Weak transcription	Gastric	stomach
6	chr14:103875400-103889600	Weak transcription	Colon Smooth Muscle	Colon
7	chr14:103875400-103892200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr14:103875400-103893600	Weak transcription	Brain Germinal Matrix	brain
9	chr14:103875600-103893800	Weak transcription	Fetal Heart	heart
10	chr14:103875600-103894000	Weak transcription	Fetal Brain Male	brain
11	chr14:103875800-103889800	Weak transcription	Lung	lung
12	chr14:103879000-103892800	Weak transcription	Spleen	Spleen
13	chr14:103879000-103895200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr14:103879000-103914200	Weak transcription	Esophagus	oesophagus
15	chr14:103879000-103941400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr14:103879600-103889400	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr14:103880400-103894200	Weak transcription	Liver	Liver
18	chr14:103880400-103904600	Weak transcription	Fetal Kidney	kidney
19	chr14:103881000-103889200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr14:103881000-103890600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr14:103881000-103900600	Weak transcription	Placenta	Placenta
22	chr14:103883000-103894400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr14:103883200-103892800	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr14:103883200-103893800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr14:103883400-103889200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr14:103883400-103889800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr14:103883400-103889800	Weak transcription	Fetal Intestine Large	intestine
28	chr14:103883400-103892800	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr14:103883400-103893600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr14:103883400-103900000	Weak transcription	Fetal Thymus	thymus
31	chr14:103883600-103888800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr14:103883600-103889200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr14:103883600-103889200	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr14:103883600-103889800	Weak transcription	Fetal Lung	lung
35	chr14:103883600-103889800	Weak transcription	Fetal Stomach	stomach
36	chr14:103883600-103892600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr14:103883600-103892800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr14:103883600-103894000	Weak transcription	Fetal Brain Female	brain
39	chr14:103883600-103894000	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr14:103883800-103889000	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr14:103883800-103892200	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr14:103883800-103894000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr14:103883800-103896800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr14:103884000-103895400	Weak transcription	Stomach Mucosa	stomach
45	chr14:103884200-103889200	Weak transcription	Ovary	ovary
46	chr14:103884200-103889200	Weak transcription	A549	lung
47	chr14:103884200-103892200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr14:103884200-103893600	Weak transcription	HUVEC	blood vessel
49	chr14:103884200-103897200	Weak transcription	Fetal Intestine Small	intestine
50	chr14:103884400-103889200	Weak transcription	Right Ventricle	heart

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