Variant report

Variant	rs7154948
Chromosome Location	chr14:104022944-104022945
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:104022338..104024927-chr14:104181805..104183745,2	MCF-7	breast:
2	chr14:104013569..104015477-chr14:104021457..104023719,2	K562	blood:
3	chr14:103991343..103994487-chr14:104021014..104023570,3	MCF-7	breast:
4	chr14:104022023..104026446-chr14:104027134..104030443,10	MCF-7	breast:
5	chr14:104021728..104024444-chr14:104089391..104091550,2	K562	blood:

Variant related genes	Relation type
ENSG00000256053	Chromatin interaction
ENSG00000126215	Chromatin interaction
ENSG00000100711	Chromatin interaction
ENSG00000126214	Chromatin interaction
ENSG00000166170	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 12 )

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

rs_ID	r²[population]
rs10134399	0.87[CEU][hapmap];0.90[GIH][hapmap];0.82[JPT][hapmap];0.95[TSI][hapmap]
rs10135248	0.80[CEU][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs10140410	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10143293	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10149249	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]
rs11621777	0.90[EUR][1000 genomes]
rs11622552	0.83[JPT][hapmap]
rs11626658	0.88[EUR][1000 genomes]
rs11626905	0.84[JPT][hapmap]
rs2274268	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2274269	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2403205	0.80[CEU][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs28513222	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28514618	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28660416	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28744517	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3783404	0.80[CEU][hapmap];0.91[JPT][hapmap]
rs55864158	0.91[EUR][1000 genomes]
rs56017123	0.89[EUR][1000 genomes]
rs57447494	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59281218	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60802358	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61996716	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61996717	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61996718	0.86[ASN][1000 genomes]
rs61996721	0.90[EUR][1000 genomes]
rs709400	0.80[CEU][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap]
rs7142883	0.89[EUR][1000 genomes]
rs7150141	0.80[CEU][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs7154587	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7693	1.00[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];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs861528	0.91[JPT][hapmap]
rs861531	0.80[CEU][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap]
rs861534	0.81[JPT][hapmap]
rs861536	0.80[CEU][hapmap];0.84[GIH][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap]
rs861539	0.84[CEU][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs942863	1.00[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];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	nsv902303	chr14:103979953-104034746	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
9	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
10	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
11	esv1839595	chr14:103987140-104034746	Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Enhancers 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	41 gene(s)	inside rSNPs	diseases
12	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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs7154948	BAG5	cis	cerebellum	SCAN
rs7154948	BAG5	cis	multi-tissue	Pritchard
rs7154948	KLC1	cis	parietal	SCAN
rs7154948	APOPT1	cis	Muscle Skeletal	GTEx
rs7154948	C14orf153	cis	parietal	SCAN
rs7154948	DIO3	cis	cerebellum	SCAN
rs7154948	MARK3	cis	Thyroid	GTEx
rs7154948	NCRNA00221	cis	parietal	SCAN
rs7154948	WDR20	cis	cerebellum	SCAN
rs7154948	ZFYVE21	cis	cerebellum	SCAN
rs7154948	C14orf153	cis	cerebellum	SCAN
rs7154948	BAG5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:103996800-104023400	Weak transcription	Primary B cells from cord blood	blood
2	chr14:104002800-104023400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr14:104007200-104024400	Weak transcription	Fetal Kidney	kidney
4	chr14:104009800-104023400	Weak transcription	Fetal Thymus	thymus
5	chr14:104010000-104023600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr14:104010200-104023600	Weak transcription	Liver	Liver
7	chr14:104010400-104023600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr14:104010600-104024200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr14:104010600-104025000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr14:104011400-104025000	Weak transcription	Ovary	ovary
11	chr14:104011400-104027800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr14:104013200-104024600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr14:104013400-104023400	Weak transcription	Dnd41	blood
14	chr14:104013600-104023000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr14:104013600-104023200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr14:104013600-104023400	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr14:104013600-104023600	Weak transcription	Primary B cells from peripheral blood	blood
18	chr14:104013600-104024200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr14:104013600-104027600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr14:104013800-104024600	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr14:104014600-104023200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr14:104016400-104023400	Weak transcription	HUVEC	blood vessel
23	chr14:104017400-104023400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr14:104017400-104024400	Weak transcription	HepG2	liver
25	chr14:104017400-104024800	Weak transcription	GM12878-XiMat	blood
26	chr14:104017400-104025800	Weak transcription	Fetal Brain Male	brain
27	chr14:104017600-104023200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr14:104017600-104027200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr14:104017800-104023400	Weak transcription	Fetal Intestine Large	intestine
30	chr14:104017800-104024800	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr14:104018200-104023400	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr14:104018200-104023400	Weak transcription	Duodenum Mucosa	Duodenum
33	chr14:104018200-104024400	Weak transcription	Primary hematopoietic stem cells	blood
34	chr14:104018200-104026200	Weak transcription	Pancreas	Pancrea
35	chr14:104018200-104026400	Weak transcription	Small Intestine	intestine
36	chr14:104018600-104023200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr14:104018600-104023600	Weak transcription	Brain Germinal Matrix	brain
38	chr14:104018600-104024400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr14:104018800-104023200	Weak transcription	Brain Cingulate Gyrus	brain
40	chr14:104018800-104023400	Weak transcription	Brain Hippocampus Middle	brain
41	chr14:104018800-104023400	Weak transcription	Fetal Lung	lung
42	chr14:104018800-104023400	Weak transcription	Placenta	Placenta
43	chr14:104019000-104023200	Weak transcription	Brain Angular Gyrus	brain
44	chr14:104019000-104023400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr14:104019000-104026800	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr14:104019200-104023200	Weak transcription	Brain Anterior Caudate	brain
47	chr14:104019200-104023200	Weak transcription	Brain Substantia Nigra	brain
48	chr14:104019200-104023400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr14:104019200-104023400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr14:104019200-104024400	Enhancers	Colon Smooth Muscle	Colon

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