Variant report

Variant	rs16860453
Chromosome Location	chr2:173330497-173330498
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:180)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:180 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr2:173330163-173330966	HepG2	liver:	n/a	n/a
2	RAD21	chr2:173330291-173330932	HCT-116	colon:	n/a	n/a
3	CTCF	chr2:173330430-173330797	A549	lung:	n/a	n/a
4	CEBPB	chr2:173330356-173330792	Hela-S3	cervix:	n/a	n/a
5	HDAC2	chr2:173330129-173330725	MCF-7	breast:	n/a	chr2:173330541-173330550
6	NFIC	chr2:173330201-173330800	HepG2	liver:	n/a	n/a
7	MAX	chr2:173330187-173330810	NB4	blood:	n/a	chr2:173330503-173330512
8	MAX	chr2:173330082-173330923	HepG2	liver:	n/a	chr2:173330503-173330512
9	MAFF	chr2:173330305-173330735	HepG2	liver:	n/a	n/a
10	RCOR1	chr2:173330214-173330788	K562	blood:	n/a	n/a
11	BATF	chr2:173330421-173330730	GM12878	blood:	n/a	n/a
12	CTCF	chr2:173330480-173330630	HFF	foreskin:	n/a	n/a
13	BHLHE40	chr2:173330178-173330784	HepG2	liver:	n/a	n/a
14	E2F6	chr2:173330244-173330501	K562	blood:	n/a	n/a
15	MYC	chr2:173330383-173330820	H1-hESC	embryonic stem cell:	n/a	chr2:173330503-173330512
16	MAX	chr2:173330144-173330756	SK-N-SH	brain:	n/a	chr2:173330503-173330512
17	CTCF	chr2:173330426-173330757	ECC-1	luminal epithelium:	n/a	n/a
18	RAD21	chr2:173330155-173330869	H1-hESC	embryonic stem cell:	n/a	n/a
19	SMC3	chr2:173330059-173330854	HepG2	liver:	n/a	n/a
20	RAD21	chr2:173330093-173330911	IMR90	lung:	n/a	n/a
21	MAFK	chr2:173330427-173330795	K562	blood:	n/a	n/a
22	CHD2	chr2:173330413-173330654	Hela-S3	cervix:	n/a	n/a
23	E2F6	chr2:173330230-173330851	H1-hESC	embryonic stem cell:	n/a	n/a
24	TBP	chr2:173330490-173330757	K562	blood:	n/a	n/a
25	CTCF	chr2:173330173-173330828	A549	lung:	n/a	n/a
26	CTCF	chr2:173330480-173330630	NHDF-neo	bronchial:	n/a	n/a
27	MXI1	chr2:173329836-173331023	SK-N-SH	brain:	n/a	n/a
28	CTCF	chr2:173330360-173330510	NHEK	skin:	n/a	n/a
29	CTCF	chr2:173330176-173330871	K562	blood:	n/a	n/a
30	CTCF	chr2:173330210-173330855	HepG2	liver:	n/a	n/a
31	CTCF	chr2:173330492-173330781	MCF-7	breast:	n/a	n/a
32	CTCF	chr2:173330188-173330886	K562	blood:	n/a	n/a
33	HDAC2	chr2:173330175-173330770	HepG2	liver:	n/a	chr2:173330541-173330550
34	CTCF	chr2:173330266-173330875	HCT-116	colon:	n/a	n/a
35	RAD21	chr2:173330333-173330936	ECC-1	luminal epithelium:	n/a	n/a
36	CEBPB	chr2:173330301-173330774	HepG2	liver:	n/a	n/a
37	JUND	chr2:173330339-173330804	K562	blood:	n/a	n/a
38	CTCF	chr2:173330380-173330530	Caco-2	colon:	n/a	n/a
39	CTCF	chr2:173330407-173330873	GM12878	blood:	n/a	n/a
40	FOXA1	chr2:173330216-173330790	HepG2	liver:	n/a	n/a
41	SIN3A	chr2:173330480-173330793	H1-hESC	embryonic stem cell:	n/a	n/a
42	ARID3A	chr2:173330138-173330802	HepG2	liver:	n/a	n/a
43	FOS	chr2:173330399-173330767	MCF10A-Er-Src	breast:	n/a	n/a
44	UBTF	chr2:173330203-173330677	K562	blood:	n/a	n/a
45	MYC	chr2:173330206-173330815	K562	blood:	n/a	chr2:173330503-173330512
46	MAX	chr2:173330193-173330787	K562	blood:	n/a	chr2:173330503-173330512
47	MXI1	chr2:173330206-173330805	HepG2	liver:	n/a	n/a
48	RAD21	chr2:173330304-173330919	MCF-7	breast:	n/a	n/a
49	FOSL2	chr2:173330164-173330732	HepG2	liver:	n/a	n/a
50	TEAD4	chr2:173330032-173330836	HepG2	liver:	n/a	n/a

No data

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:171785240..171786018-chr2:173330491..173331047,2	MCF-7	breast:

No data

Variant related genes	Relation type
ITGA6	TF binding region
ENSG00000115806	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs16860433	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16860500	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16860505	1.00[AMR][1000 genomes]
rs16860517	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16860530	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16860562	1.00[AMR][1000 genomes]
rs16860566	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16860616	1.00[AMR][1000 genomes]
rs16860730	1.00[AMR][1000 genomes]
rs28653613	1.00[AMR][1000 genomes]
rs34599583	1.00[AMR][1000 genomes]
rs73023431	1.00[AMR][1000 genomes]
rs73023468	1.00[AMR][1000 genomes]
rs73023472	1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173319200-173330600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr2:173321400-173356000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:173324400-173330600	Enhancers	HUVEC	blood vessel
4	chr2:173326000-173330600	Enhancers	Primary B cells from peripheral blood	blood
5	chr2:173326000-173330600	Enhancers	Fetal Intestine Large	intestine
6	chr2:173326000-173330600	Enhancers	Fetal Thymus	thymus
7	chr2:173326000-173330600	Enhancers	Sigmoid Colon	Sigmoid Colon
8	chr2:173326400-173340400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:173326600-173330600	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr2:173327200-173330600	Enhancers	Dnd41	blood
11	chr2:173327200-173353200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:173327400-173338600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr2:173327400-173345000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:173327600-173330600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:173327800-173333200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr2:173327800-173370800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr2:173328000-173330600	Enhancers	Stomach Mucosa	stomach
18	chr2:173328000-173335800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr2:173328200-173330600	Enhancers	Placenta Amnion	Placenta Amnion
20	chr2:173328200-173331000	Genic enhancers	HMEC	breast
21	chr2:173328600-173330600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr2:173328600-173330800	Enhancers	Primary T cells fromperipheralblood	blood
23	chr2:173328600-173331000	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr2:173328800-173330800	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr2:173328800-173330800	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr2:173328800-173331200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr2:173328800-173332200	Weak transcription	Spleen	Spleen
28	chr2:173328800-173339000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr2:173328800-173353400	Weak transcription	Right Ventricle	heart
30	chr2:173329000-173330600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr2:173329000-173332200	Weak transcription	Pancreas	Pancrea
32	chr2:173329000-173335800	Weak transcription	Gastric	stomach
33	chr2:173329000-173335800	Weak transcription	Lung	lung
34	chr2:173329400-173330600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
35	chr2:173329400-173330600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
36	chr2:173329400-173331000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr2:173329400-173331200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr2:173329400-173335800	Weak transcription	Left Ventricle	heart
39	chr2:173329400-173344400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr2:173329800-173330600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr2:173329800-173330600	Enhancers	Liver	Liver
42	chr2:173329800-173330600	Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr2:173329800-173330600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
44	chr2:173329800-173371200	Weak transcription	Hela-S3	cervix
45	chr2:173330000-173330600	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr2:173330000-173330600	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
47	chr2:173330000-173330600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr2:173330000-173330600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
49	chr2:173330000-173330600	Enhancers	Adipose Nuclei	Adipose
50	chr2:173330000-173330600	Active TSS	Brain Inferior Temporal Lobe	brain

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