Variant report

Variant	rs12498216
Chromosome Location	chr4:57864022-57864023
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr4:57863890-57864129	HepG2	liver:	n/a	chr4:57863996-57864007 chr4:57863994-57864008 chr4:57863995-57864011 chr4:57864000-57864009 chr4:57863995-57864006 chr4:57863995-57864006
2	POLR2A	chr4:57863913-57864279	K562	blood:	n/a	n/a
3	POLR2A	chr4:57863754-57864242	K562	blood:	n/a	n/a
4	MAFF	chr4:57863953-57864048	HepG2	liver:	n/a	chr4:57863993-57864011
5	POLR2A	chr4:57863783-57864122	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:57849127..57850775-chr4:57862388..57864850,2	K562	blood:
2	chr4:57856196..57858263-chr4:57863410..57864964,2	K562	blood:
3	chr4:57843709..57847231-chr4:57862818..57866866,4	K562	blood:
4	chr4:57849127..57851147-chr4:57863350..57865487,2	K562	blood:
5	chr4:57859120..57861097-chr4:57862299..57864357,2	K562	blood:

Variant related genes	Relation type
RNU6-998P	TF binding region
ENSG00000084092	Chromatin interaction
ENSG00000238579	Chromatin interaction
ENSG00000047315	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10000395	0.84[ASN][1000 genomes]
rs10023088	0.83[ASN][1000 genomes]
rs10461349	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1056364	0.83[ASN][1000 genomes]
rs11573125	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11573126	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12506598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12512295	0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12621	0.90[ASN][1000 genomes]
rs12650737	0.81[ASN][1000 genomes]
rs1277308	0.90[ASN][1000 genomes]
rs1403233	0.92[ASN][1000 genomes]
rs1626594	0.93[ASN][1000 genomes]
rs1713982	0.92[ASN][1000 genomes]
rs1713983	0.92[ASN][1000 genomes]
rs1718830	0.92[ASN][1000 genomes]
rs1718831	0.92[ASN][1000 genomes]
rs1718837	0.93[ASN][1000 genomes]
rs1718863	0.92[ASN][1000 genomes]
rs1718864	0.92[ASN][1000 genomes]
rs1718878	0.93[ASN][1000 genomes]
rs2276897	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2412774	0.90[ASN][1000 genomes]
rs3775082	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3796532	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3821994	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4864609	0.93[ASN][1000 genomes]
rs4865169	0.83[ASN][1000 genomes]
rs56763474	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60292561	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61337636	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67479587	0.93[ASN][1000 genomes]
rs6843644	0.89[ASN][1000 genomes]
rs73167819	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73167841	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9918067	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv1012125	chr4:57668229-57865803	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv964049	chr4:57858281-57871268	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57846000-57881000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:57846800-57900000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:57848400-57875200	Weak transcription	Stomach Mucosa	stomach
4	chr4:57848600-57900000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr4:57849000-57900000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr4:57849200-57869000	Strong transcription	Primary B cells from peripheral blood	blood
7	chr4:57849200-57886200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr4:57849600-57884600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr4:57850600-57870200	Strong transcription	GM12878-XiMat	blood
10	chr4:57850600-57899400	Strong transcription	Fetal Thymus	thymus
11	chr4:57850800-57899400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr4:57851000-57899200	Strong transcription	Primary T cells from cord blood	blood
13	chr4:57851000-57899400	Strong transcription	Duodenum Mucosa	Duodenum
14	chr4:57851200-57897200	Strong transcription	Fetal Intestine Large	intestine
15	chr4:57851400-57894800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr4:57851600-57864400	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr4:57851600-57899400	Strong transcription	Placenta	Placenta
18	chr4:57851800-57868600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr4:57851800-57899400	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr4:57851800-57899400	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr4:57851800-57899400	Strong transcription	Liver	Liver
22	chr4:57851800-57899600	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr4:57852000-57892200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr4:57852000-57894800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr4:57852000-57898200	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr4:57852200-57899000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr4:57852200-57899400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr4:57852600-57899400	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr4:57856000-57868400	Strong transcription	HMEC	breast
30	chr4:57856000-57870800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr4:57856000-57871800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr4:57856000-57899400	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr4:57856200-57866000	Weak transcription	Right Ventricle	heart
34	chr4:57856200-57886200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr4:57856800-57869200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
36	chr4:57856800-57900000	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr4:57858200-57899800	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr4:57858400-57899800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr4:57858400-57899800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr4:57859000-57898000	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr4:57859400-57898600	Strong transcription	Dnd41	blood
42	chr4:57859600-57864200	Strong transcription	A549	lung
43	chr4:57859600-57864400	Strong transcription	HepG2	liver
44	chr4:57859600-57881800	Strong transcription	Primary B cells from cord blood	blood
45	chr4:57859600-57897800	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr4:57860000-57864400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr4:57860000-57865200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr4:57860200-57885000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr4:57860200-57898800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr4:57860600-57892800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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