Variant report

Variant	rs28660416
Chromosome Location	chr14:104044215-104044216
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:104002192..104004863-chr14:104043017..104044904,2	K562	blood:
2	chr14:104040497..104046116-chr14:104179984..104183762,7	MCF-7	breast:
3	chr14:104043082..104044725-chr14:104094737..104096881,2	MCF-7	breast:
4	chr14:104037950..104041311-chr14:104041482..104045327,4	MCF-7	breast:

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

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10134399	0.82[EUR][1000 genomes]
rs10140410	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10143293	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10149249	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11621777	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11626658	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2274268	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2274269	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28513222	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28514618	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28744517	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55864158	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56017123	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57447494	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59281218	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60802358	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61996716	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61996717	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61996718	0.89[ASN][1000 genomes]
rs61996721	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7142883	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7154587	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7154948	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7693	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs942863	0.82[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28660416	APOPT1	cis	Muscle Skeletal	GTEx
rs28660416	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	chr14:104030000-104045000	Weak transcription	Aorta	Aorta
2	chr14:104030200-104044800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr14:104030800-104073200	Weak transcription	Small Intestine	intestine
4	chr14:104035400-104060400	Weak transcription	Fetal Brain Male	brain
5	chr14:104037400-104048400	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr14:104037800-104045400	Strong transcription	Primary T helper cells fromperipheralblood	blood
7	chr14:104038000-104045600	Strong transcription	Primary B cells from peripheral blood	blood
8	chr14:104038000-104045600	Strong transcription	Dnd41	blood
9	chr14:104038400-104048800	Strong transcription	Fetal Brain Female	brain
10	chr14:104038400-104049400	Strong transcription	Primary T cells from cord blood	blood
11	chr14:104038800-104045600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr14:104038800-104045600	Strong transcription	HepG2	liver
13	chr14:104038800-104045600	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr14:104038800-104046000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr14:104038800-104051000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr14:104039000-104045800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr14:104039000-104046400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr14:104039200-104045600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr14:104039400-104045600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr14:104039400-104045800	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr14:104039600-104045400	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr14:104039800-104045600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr14:104040000-104045600	Strong transcription	Thymus	Thymus
24	chr14:104040200-104045600	Strong transcription	Primary B cells from cord blood	blood
25	chr14:104041000-104059600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr14:104041000-104063200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr14:104041200-104044600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr14:104041600-104044600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr14:104041600-104056200	Weak transcription	K562	blood
30	chr14:104041600-104056400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr14:104041800-104044600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr14:104041800-104044600	Weak transcription	Fetal Thymus	thymus
33	chr14:104041800-104044600	Weak transcription	GM12878-XiMat	blood
34	chr14:104041800-104052600	Weak transcription	Psoas Muscle	Psoas
35	chr14:104041800-104059600	Weak transcription	Primary hematopoietic stem cells	blood
36	chr14:104041800-104060600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr14:104042000-104044400	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr14:104042000-104044600	Weak transcription	Esophagus	oesophagus
39	chr14:104042200-104044800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr14:104042200-104057200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr14:104042600-104045600	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr14:104042800-104045400	Genic enhancers	Spleen	Spleen
43	chr14:104042800-104045600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr14:104043000-104044400	Weak transcription	Fetal Kidney	kidney
45	chr14:104043000-104045800	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr14:104043200-104044800	Weak transcription	HSMMtube	muscle
47	chr14:104043200-104045000	Weak transcription	Pancreas	Pancrea
48	chr14:104043200-104045600	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr14:104043200-104046400	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr14:104043400-104044600	Weak transcription	Brain Hippocampus Middle	brain

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