Variant report

Variant	rs16860457
Chromosome Location	chr2:173330807-173330808
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:79)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:79 , 50 per page) page: 1 2

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	MAX	chr2:173330187-173330810	NB4	blood:	n/a	chr2:173330503-173330512
4	MAX	chr2:173330082-173330923	HepG2	liver:	n/a	chr2:173330503-173330512
5	MYC	chr2:173330383-173330820	H1-hESC	embryonic stem cell:	n/a	chr2:173330503-173330512
6	RAD21	chr2:173330155-173330869	H1-hESC	embryonic stem cell:	n/a	n/a
7	SMC3	chr2:173330059-173330854	HepG2	liver:	n/a	n/a
8	RAD21	chr2:173330093-173330911	IMR90	lung:	n/a	n/a
9	E2F6	chr2:173330230-173330851	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr2:173330173-173330828	A549	lung:	n/a	n/a
11	MXI1	chr2:173329836-173331023	SK-N-SH	brain:	n/a	n/a
12	CTCF	chr2:173330176-173330871	K562	blood:	n/a	n/a
13	CTCF	chr2:173330210-173330855	HepG2	liver:	n/a	n/a
14	CTCF	chr2:173330188-173330886	K562	blood:	n/a	n/a
15	CTCF	chr2:173330266-173330875	HCT-116	colon:	n/a	n/a
16	RAD21	chr2:173330333-173330936	ECC-1	luminal epithelium:	n/a	n/a
17	CTCF	chr2:173330407-173330873	GM12878	blood:	n/a	n/a
18	MYC	chr2:173330206-173330815	K562	blood:	n/a	chr2:173330503-173330512
19	RAD21	chr2:173330304-173330919	MCF-7	breast:	n/a	n/a
20	TEAD4	chr2:173330032-173330836	HepG2	liver:	n/a	n/a
21	CTCF	chr2:173329937-173331141	SK-N-SH	brain:	n/a	n/a
22	SMC3	chr2:173330085-173331034	SK-N-SH	brain:	n/a	n/a
23	SMC3	chr2:173330338-173330830	Hela-S3	cervix:	n/a	n/a
24	MAX	chr2:173330033-173330910	A549	lung:	n/a	chr2:173330503-173330512
25	CTCF	chr2:173330502-173330817	Spleen_OC	spleen:	n/a	n/a
26	CTCF	chr2:173330340-173330894	MCF-7	breast:	n/a	n/a
27	FOXA1	chr2:173330129-173331027	HepG2	liver:	n/a	n/a
28	NFIC	chr2:173330130-173330846	HepG2	liver:	n/a	n/a
29	FOSL2	chr2:173330176-173330838	HepG2	liver:	n/a	n/a
30	CTCF	chr2:173330190-173330905	MCF-7	breast:	n/a	n/a
31	EP300	chr2:173330172-173330845	HepG2	liver:	n/a	chr2:173330501-173330515
32	RCOR1	chr2:173330218-173330850	HepG2	liver:	n/a	n/a
33	MXI1	chr2:173330027-173331135	IMR90	lung:	n/a	n/a
34	SMC3	chr2:173330444-173330825	GM12878	blood:	n/a	n/a
35	SP1	chr2:173330315-173330843	A549	lung:	n/a	n/a
36	RAD21	chr2:173330332-173330928	ECC-1	luminal epithelium:	n/a	n/a
37	CTCF	chr2:173330414-173330833	H1-hESC	embryonic stem cell:	n/a	n/a
38	ZMIZ1	chr2:173330429-173330817	K562	blood:	n/a	n/a
39	MAX	chr2:173330335-173330827	H1-hESC	embryonic stem cell:	n/a	chr2:173330503-173330512
40	RAD21	chr2:173330238-173330877	H1-hESC	embryonic stem cell:	n/a	n/a
41	CTCF	chr2:173329954-173331103	A549	lung:	n/a	n/a
42	MAZ	chr2:173330168-173330892	HepG2	liver:	n/a	chr2:173330503-173330512
43	MYC	chr2:173330079-173330989	A549	lung:	n/a	chr2:173330503-173330512
44	CEBPB	chr2:173330124-173330855	A549	lung:	n/a	n/a
45	RAD21	chr2:173330167-173330963	MCF-7	breast:	n/a	n/a
46	MYC	chr2:173330165-173330820	NB4	blood:	n/a	chr2:173330503-173330512
47	RAD21	chr2:173330239-173330858	HepG2	liver:	n/a	n/a
48	MBD4	chr2:173330145-173330867	HepG2	liver:	n/a	n/a
49	CTCF	chr2:173330465-173330814	SK-N-SH_RA	brain:	n/a	n/a
50	STAT3	chr2:173330486-173330809	Hela-S3	cervix:	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
ENSG00000232788	TF binding region
ITGA6	TF binding region
ENSG00000115806	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs16860448	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs16860456	1.00[AMR][1000 genomes]
rs16860507	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs16860522	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs16860527	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16860571	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs16860583	0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs16860592	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs16860625	0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs16860635	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2737085	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57121932	0.85[AMR][1000 genomes]
rs57528312	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs60715604	0.85[AMR][1000 genomes]
rs61403555	0.85[AMR][1000 genomes]
rs6715727	0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6741374	0.85[AMR][1000 genomes]
rs6754798	0.85[AMR][1000 genomes]
rs7557427	0.85[AMR][1000 genomes]
rs7588603	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7603135	0.87[YRI][hapmap];0.87[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:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173321400-173356000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:173326400-173340400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr2:173327200-173353200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:173327400-173338600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:173327400-173345000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:173327800-173333200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr2:173327800-173370800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:173328000-173335800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr2:173328200-173331000	Genic enhancers	HMEC	breast
10	chr2:173328600-173331000	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr2:173328800-173331200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr2:173328800-173332200	Weak transcription	Spleen	Spleen
13	chr2:173328800-173339000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr2:173328800-173353400	Weak transcription	Right Ventricle	heart
15	chr2:173329000-173332200	Weak transcription	Pancreas	Pancrea
16	chr2:173329000-173335800	Weak transcription	Gastric	stomach
17	chr2:173329000-173335800	Weak transcription	Lung	lung
18	chr2:173329400-173331000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr2:173329400-173331200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr2:173329400-173335800	Weak transcription	Left Ventricle	heart
21	chr2:173329400-173344400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:173329800-173371200	Weak transcription	Hela-S3	cervix
23	chr2:173330000-173332200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr2:173330200-173335800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr2:173330200-173342200	Weak transcription	Brain Substantia Nigra	brain
26	chr2:173330200-173345600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr2:173330200-173350400	Weak transcription	Primary B cells from cord blood	blood
28	chr2:173330400-173331000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr2:173330400-173331400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr2:173330400-173331800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr2:173330400-173332000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr2:173330400-173332600	Strong transcription	Fetal Intestine Small	intestine
33	chr2:173330400-173335800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr2:173330400-173339400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr2:173330400-173360400	Weak transcription	Small Intestine	intestine
36	chr2:173330600-173331000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr2:173330600-173331000	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr2:173330600-173331000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr2:173330600-173331000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:173330600-173331000	Enhancers	Brain Cingulate Gyrus	brain
41	chr2:173330600-173331000	Weak transcription	Duodenum Mucosa	Duodenum
42	chr2:173330600-173331000	Genic enhancers	Rectal Mucosa Donor 29	rectum
43	chr2:173330600-173331000	Genic enhancers	HepG2	liver
44	chr2:173330600-173331000	Genic enhancers	HSMM	muscle
45	chr2:173330600-173331000	Enhancers	NHDF-Ad	bronchial
46	chr2:173330600-173331200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr2:173330600-173331400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr2:173330600-173331600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr2:173330600-173331800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr2:173330600-173331800	Weak transcription	Colonic Mucosa	Colon

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