Variant report

Variant	rs4900586
Chromosome Location	chr14:104119701-104119702
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:104094508..104097348-chr14:104119011..104121008,3	MCF-7	breast:
2	chr14:104078874..104081793-chr14:104117950..104120099,2	MCF-7	breast:
3	chr14:104116587..104120491-chr14:104126433..104129396,3	K562	blood:
4	chr14:104091249..104097746-chr14:104118497..104125842,12	MCF-7	breast:
5	chr14:104116747..104120197-chr14:104121939..104124709,3	K562	blood:

Variant related genes	Relation type
ENSG00000126214	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10047805	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10131067	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1054080	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11160756	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11626589	0.85[ASN][1000 genomes]
rs11848721	0.86[ASN][1000 genomes]
rs11850979	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2403203	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28798508	0.84[ASN][1000 genomes]
rs28823639	0.84[ASN][1000 genomes]
rs2896488	0.85[ASN][1000 genomes]
rs2896489	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35015260	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3742463	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3742465	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3759586	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4374097	0.84[ASN][1000 genomes]
rs4383078	0.84[ASN][1000 genomes]
rs4444269	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4464019	0.81[ASN][1000 genomes]
rs4561394	0.82[ASN][1000 genomes]
rs4900589	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4906341	0.86[ASN][1000 genomes]
rs4906348	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4906355	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4906358	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61436277	0.84[ASN][1000 genomes]
rs61995761	0.86[ASN][1000 genomes]
rs709399	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7154572	0.82[ASN][1000 genomes]
rs7156832	0.81[ASN][1000 genomes]
rs7157116	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7161125	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs729437	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs745079	0.84[ASN][1000 genomes]
rs8003289	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8007915	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8008451	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8018214	0.81[ASN][1000 genomes]
rs8020099	0.80[ASN][1000 genomes]
rs8021368	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8021904	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs861530	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs861537	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs861544	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs861545	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs861547	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8702	0.92[AMR][1000 genomes];0.91[EUR][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	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	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
4	nsv1052010	chr14:104061472-104216267	Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv542201	chr14:104061472-104216267	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv456435	chr14:104061646-104198251	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
7	nsv566023	chr14:104061646-104198251	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
8	nsv902308	chr14:104087209-104211180	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
9	nsv1041329	chr14:104097750-104196346	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
10	nsv542202	chr14:104097750-104196346	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
11	nsv1048866	chr14:104100862-104195896	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
12	nsv542203	chr14:104113463-104143782	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4900586	BAG5	Cis_1M	lymphoblastoid	RTeQTL
rs4900586	ZFYVE21	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104097400-104120000	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr14:104097400-104120000	Weak transcription	HUVEC	blood vessel
3	chr14:104097400-104120200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr14:104097400-104120200	Weak transcription	Colonic Mucosa	Colon
5	chr14:104097400-104120200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr14:104097400-104120400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr14:104097400-104120400	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr14:104097400-104120800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr14:104097400-104156600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr14:104098600-104119800	Weak transcription	K562	blood
11	chr14:104099200-104120200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr14:104101000-104120200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr14:104101200-104120600	Weak transcription	Brain Germinal Matrix	brain
14	chr14:104101800-104120800	Weak transcription	Hela-S3	cervix
15	chr14:104102600-104120000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr14:104104600-104120200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr14:104104800-104120200	Weak transcription	Fetal Intestine Large	intestine
18	chr14:104104800-104120400	Weak transcription	Liver	Liver
19	chr14:104104800-104120800	Weak transcription	HepG2	liver
20	chr14:104105200-104120200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr14:104105200-104121800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr14:104105200-104122200	Weak transcription	Fetal Kidney	kidney
23	chr14:104105400-104120000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr14:104105400-104120200	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr14:104105400-104120200	Weak transcription	Duodenum Mucosa	Duodenum
26	chr14:104105400-104120400	Weak transcription	Fetal Brain Male	brain
27	chr14:104105600-104120000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr14:104107800-104120200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr14:104107800-104120200	Weak transcription	Fetal Brain Female	brain
30	chr14:104108000-104120800	Weak transcription	HMEC	breast
31	chr14:104108000-104130000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr14:104109000-104120400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr14:104110000-104122200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr14:104110400-104120400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr14:104110800-104130000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr14:104112000-104120400	Weak transcription	Primary B cells from peripheral blood	blood
37	chr14:104113200-104120200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr14:104113200-104120200	Weak transcription	GM12878-XiMat	blood
39	chr14:104113200-104120800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr14:104115600-104119800	Weak transcription	Fetal Muscle Trunk	muscle
41	chr14:104117600-104120800	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr14:104117600-104121800	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr14:104117800-104120200	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr14:104117800-104120400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr14:104117800-104120600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr14:104117800-104120600	Enhancers	Brain Angular Gyrus	brain
47	chr14:104117800-104120600	Enhancers	Fetal Heart	heart
48	chr14:104117800-104120600	Enhancers	Right Atrium	heart
49	chr14:104117800-104120800	Enhancers	Brain Cingulate Gyrus	brain
50	chr14:104117800-104120800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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