Variant report

Variant	rs4889425
Chromosome Location	chr16:81924054-81924055
allele	C/T
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	SP1	chr16:81923623-81924270	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr16:81924040-81924190	GM12872	blood:	n/a	chr16:81924142-81924158 chr16:81924143-81924164 chr16:81924146-81924154 chr16:81924141-81924159
3	GATA3	chr16:81923405-81924276	MCF-7	breast:	n/a	n/a
4	ZNF143	chr16:81923976-81924342	H1-hESC	embryonic stem cell:	n/a	n/a
5	RAD21	chr16:81923974-81924358	K562	blood:	n/a	chr16:81924144-81924151 chr16:81924142-81924161 chr16:81924146-81924155
6	CTCF	chr16:81924019-81924269	Lung_OC	lung:	n/a	chr16:81924142-81924158 chr16:81924143-81924164 chr16:81924146-81924154 chr16:81924141-81924159
7	RAD21	chr16:81923978-81924370	ECC-1	luminal epithelium:	n/a	chr16:81924144-81924151 chr16:81924142-81924161 chr16:81924146-81924155
8	FOS	chr16:81924006-81924297	MCF10A-Er-Src	breast:	n/a	n/a
9	CTCF	chr16:81923965-81924228	ECC-1	luminal epithelium:	n/a	chr16:81924142-81924158 chr16:81924143-81924164 chr16:81924146-81924154 chr16:81924141-81924159
10	CTCF	chr16:81924027-81924278	GM13977	blood:	n/a	chr16:81924142-81924158 chr16:81924143-81924164 chr16:81924146-81924154 chr16:81924141-81924159
11	CTCF	chr16:81924040-81924190	HCM	heart:	n/a	chr16:81924142-81924158 chr16:81924143-81924164 chr16:81924146-81924154 chr16:81924141-81924159
12	CTCF	chr16:81924012-81924287	GM10266	blood:	n/a	chr16:81924142-81924158 chr16:81924143-81924164 chr16:81924146-81924154 chr16:81924141-81924159
13	FOXA1	chr16:81923671-81924294	T-47D	breast:	n/a	chr16:81924130-81924142
14	CTCF	chr16:81924020-81924278	Hela-S3	cervix:	n/a	chr16:81924142-81924158 chr16:81924143-81924164 chr16:81924146-81924154 chr16:81924141-81924159
15	CEBPB	chr16:81923984-81924320	Hela-S3	cervix:	n/a	n/a
16	CTCF	chr16:81923898-81924330	H1-hESC	embryonic stem cell:	n/a	chr16:81924142-81924158 chr16:81924143-81924164 chr16:81924146-81924154 chr16:81924141-81924159
17	CTCF	chr16:81923892-81924323	HepG2	liver:	n/a	chr16:81924142-81924158 chr16:81924143-81924164 chr16:81924146-81924154 chr16:81924141-81924159
18	CTCF	chr16:81924024-81924288	MCF-7	breast:	n/a	chr16:81924142-81924158 chr16:81924143-81924164 chr16:81924146-81924154 chr16:81924141-81924159
19	RAD21	chr16:81923802-81924458	MCF-7	breast:	n/a	chr16:81924144-81924151 chr16:81924142-81924161 chr16:81924146-81924155
20	CTCF	chr16:81924006-81924272	Pancreas_OC	pancreas:	n/a	chr16:81924142-81924158 chr16:81924143-81924164 chr16:81924146-81924154 chr16:81924141-81924159
21	CTCF	chr16:81924011-81924304	MCF-7	breast:	n/a	chr16:81924142-81924158 chr16:81924143-81924164 chr16:81924146-81924154 chr16:81924141-81924159
22	MAZ	chr16:81923988-81924328	K562	blood:	n/a	n/a
23	CTCF	chr16:81924040-81924190	HA-sp	spinal cord:	n/a	chr16:81924142-81924158 chr16:81924143-81924164 chr16:81924146-81924154 chr16:81924141-81924159
24	CTCF	chr16:81924051-81924222	GM20000	blood:	n/a	chr16:81924142-81924158 chr16:81924143-81924164 chr16:81924146-81924154 chr16:81924141-81924159
25	RAD21	chr16:81923961-81924378	H1-hESC	embryonic stem cell:	n/a	chr16:81924144-81924151 chr16:81924142-81924161 chr16:81924146-81924155
26	CTCF	chr16:81924010-81924289	HepG2	liver:	n/a	chr16:81924142-81924158 chr16:81924143-81924164 chr16:81924146-81924154 chr16:81924141-81924159
27	CTCF	chr16:81924040-81924297	A549	lung:	n/a	chr16:81924142-81924158 chr16:81924143-81924164 chr16:81924146-81924154 chr16:81924141-81924159
28	RAD21	chr16:81923864-81924519	A549	lung:	n/a	chr16:81924144-81924151 chr16:81924142-81924161 chr16:81924146-81924155
29	CTCF	chr16:81923958-81924354	A549	lung:	n/a	chr16:81924142-81924158 chr16:81924143-81924164 chr16:81924146-81924154 chr16:81924141-81924159
30	RAD21	chr16:81923903-81924380	H1-hESC	embryonic stem cell:	n/a	chr16:81924144-81924151 chr16:81924142-81924161 chr16:81924146-81924155
31	RAD21	chr16:81923960-81924292	SK-N-SH_RA	brain:	n/a	chr16:81924144-81924151 chr16:81924142-81924161 chr16:81924146-81924155
32	CTCF	chr16:81924034-81924300	NHEK	skin:	n/a	chr16:81924142-81924158 chr16:81924143-81924164 chr16:81924146-81924154 chr16:81924141-81924159
33	RAD21	chr16:81923866-81924440	A549	lung:	n/a	chr16:81924144-81924151 chr16:81924142-81924161 chr16:81924146-81924155
34	CTCF	chr16:81924000-81924150	HCM	heart:	n/a	n/a
35	CTCF	chr16:81924030-81924264	Kidney_OC	kidney:	n/a	chr16:81924142-81924158 chr16:81924143-81924164 chr16:81924146-81924154 chr16:81924141-81924159
36	RAD21	chr16:81923995-81924278	K562	blood:	n/a	chr16:81924144-81924151 chr16:81924142-81924161 chr16:81924146-81924155
37	FOXA2	chr16:81923729-81924254	HepG2	liver:	n/a	chr16:81924130-81924142
38	CTCF	chr16:81923994-81924269	T-47D	breast:	n/a	chr16:81924142-81924158 chr16:81924143-81924164 chr16:81924146-81924154 chr16:81924141-81924159
39	RAD21	chr16:81924046-81924320	GM12878	blood:	n/a	chr16:81924144-81924151 chr16:81924142-81924161 chr16:81924146-81924155
40	STAT1	chr16:81924044-81924194	GM12878	blood:	n/a	n/a
41	RAD21	chr16:81923880-81924343	HepG2	liver:	n/a	chr16:81924144-81924151 chr16:81924142-81924161 chr16:81924146-81924155
42	POLR2A	chr16:81923742-81924368	GM12878	blood:	n/a	n/a
43	RAD21	chr16:81923997-81924300	SK-N-SH_RA	brain:	n/a	chr16:81924144-81924151 chr16:81924142-81924161 chr16:81924146-81924155
44	CTCF	chr16:81924047-81924305	GM19238	blood:	n/a	chr16:81924142-81924158 chr16:81924143-81924164 chr16:81924146-81924154 chr16:81924141-81924159
45	CTCF	chr16:81924018-81924271	SK-N-SH_RA	brain:	n/a	chr16:81924142-81924158 chr16:81924143-81924164 chr16:81924146-81924154 chr16:81924141-81924159
46	CTCF	chr16:81923974-81924301	Medullo	brain:	n/a	chr16:81924142-81924158 chr16:81924143-81924164 chr16:81924146-81924154 chr16:81924141-81924159
47	GATA3	chr16:81923468-81924282	T-47D	breast:	n/a	n/a
48	CTCF	chr16:81923974-81924311	A549	lung:	n/a	chr16:81924142-81924158 chr16:81924143-81924164 chr16:81924146-81924154 chr16:81924141-81924159
49	RCOR1	chr16:81923647-81924304	K562	blood:	n/a	n/a
50	CTCF	chr16:81924020-81924170	GM12875	blood:	n/a	chr16:81924142-81924158 chr16:81924143-81924164 chr16:81924146-81924154 chr16:81924141-81924159

No.	Distal block	Cell Line	Cell type
1	chr16:81923752..81924641-chr16:82028156..82028916,2	MCF-7	breast:
2	chr16:81923730..81925086-chr16:81972697..81973538,4	MCF-7	breast:
3	chr16:81923808..81924601-chr16:81966050..81966774,2	MCF-7	breast:
4	chr16:81923547..81924618-chr16:82095228..82096136,4	K562	blood:
5	chr16:81923911..81924649-chr16:82263311..82264070,2	K562	blood:
6	chr16:81923846..81924603-chr7:99698923..99699554,2	NB4	blood:
7	chr16:81923763..81924551-chr16:81972966..81973650,4	MCF-7	breast:

Variant related genes	Relation type
PLCG2	TF binding region
ENSG00000166508	Chromatin interaction
ENSG00000221838	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs16956020	1.00[JPT][hapmap]
rs4133125	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4414487	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4889427	1.00[JPT][hapmap]
rs4889428	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs61322346	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62043998	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8191047	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv573365	chr16:81804972-81975892	Strong transcription Bivalent/Poised TSS Weak transcription ZNF genes & repeats Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv1065088	chr16:81878481-81953248	Enhancers ZNF genes & repeats Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:81899000-81934600	Weak transcription	Right Atrium	heart
2	chr16:81900800-81925000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr16:81901000-81929200	Weak transcription	Brain Substantia Nigra	brain
4	chr16:81901200-81925000	Weak transcription	Adipose Nuclei	Adipose
5	chr16:81902800-81955600	Weak transcription	Fetal Kidney	kidney
6	chr16:81905800-81943000	Weak transcription	Small Intestine	intestine
7	chr16:81907800-81925000	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr16:81908000-81924400	Weak transcription	Colon Smooth Muscle	Colon
9	chr16:81908200-81925000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr16:81908200-81936800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr16:81908400-81950000	Strong transcription	GM12878-XiMat	blood
12	chr16:81908400-81950200	Strong transcription	Primary B cells from peripheral blood	blood
13	chr16:81909400-81961800	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr16:81911400-81936400	Weak transcription	Pancreas	Pancrea
15	chr16:81913400-81934000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr16:81917600-81925000	Weak transcription	Lung	lung
17	chr16:81918000-81924800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr16:81919400-81935600	Strong transcription	Primary B cells from cord blood	blood
19	chr16:81920400-81982000	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr16:81921200-81924400	Enhancers	HepG2	liver
21	chr16:81921200-81935600	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr16:81921800-81932200	Strong transcription	Spleen	Spleen
23	chr16:81922400-81924800	Weak transcription	Fetal Intestine Small	intestine
24	chr16:81922400-81930200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr16:81922400-81944800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr16:81922800-81929200	Weak transcription	Gastric	stomach
27	chr16:81923000-81924400	Flanking Active TSS	Liver	Liver
28	chr16:81923000-81936800	Weak transcription	Placenta	Placenta
29	chr16:81923600-81924400	Enhancers	H1 Cell Line	embryonic stem cell
30	chr16:81923600-81924400	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr16:81923600-81924400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr16:81923600-81924400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr16:81923600-81924400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr16:81923800-81924200	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr16:81923800-81924200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr16:81923800-81924400	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr16:81923800-81924400	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr16:81923800-81924400	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr16:81923800-81924400	Genic enhancers	Duodenum Mucosa	Duodenum
40	chr16:81923800-81924400	Enhancers	Fetal Intestine Large	intestine
41	chr16:81923800-81924400	Enhancers	Stomach Mucosa	stomach
42	chr16:81923800-81924400	Enhancers	A549	lung
43	chr16:81923800-81934600	Weak transcription	Thymus	Thymus
44	chr16:81924000-81924200	Weak transcription	Primary hematopoietic stem cells	blood
45	chr16:81924000-81924200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr16:81924000-81924400	Enhancers	K562	blood
47	chr16:81924000-81924600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr16:81924000-81925000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr16:81924000-81930200	Weak transcription	Rectal Mucosa Donor 31	rectum

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