Variant report

Variant	rs28898594
Chromosome Location	chr2:234620233-234620234
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	CTCF	chr2:234620140-234620290	HVMF	connective:	n/a	chr2:234620245-234620261 chr2:234620246-234620259 chr2:234620246-234620259 chr2:234620244-234620262 chr2:234620239-234620260 chr2:234620247-234620257 chr2:234620250-234620259
2	MYC	chr2:234620095-234620270	K562	blood:	n/a	n/a
3	CTCF	chr2:234620114-234620399	MCF-7	breast:	n/a	chr2:234620245-234620261 chr2:234620246-234620259 chr2:234620246-234620259 chr2:234620244-234620262 chr2:234620239-234620260 chr2:234620247-234620257 chr2:234620250-234620259
4	RAD21	chr2:234620013-234620442	H1-hESC	embryonic stem cell:	n/a	chr2:234620248-234620257 chr2:234620242-234620261 chr2:234620244-234620256
5	CTCF	chr2:234620200-234620350	GM12875	blood:	n/a	chr2:234620245-234620261 chr2:234620246-234620259 chr2:234620246-234620259 chr2:234620244-234620262 chr2:234620239-234620260 chr2:234620247-234620257 chr2:234620250-234620259
6	CTCF	chr2:234620160-234620310	AG10803	skin:	n/a	chr2:234620245-234620261 chr2:234620246-234620259 chr2:234620246-234620259 chr2:234620244-234620262 chr2:234620239-234620260 chr2:234620247-234620257 chr2:234620250-234620259
7	GTF2F1	chr2:234620097-234620388	Hela-S3	cervix:	n/a	n/a
8	MYC	chr2:234620204-234620317	HUVEC	blood vessel:	n/a	n/a
9	CTCF	chr2:234620111-234620434	Lung_OC	lung:	n/a	chr2:234620245-234620261 chr2:234620246-234620259 chr2:234620246-234620259 chr2:234620244-234620262 chr2:234620239-234620260 chr2:234620247-234620257 chr2:234620250-234620259
10	BHLHE40	chr2:234620203-234620396	GM12878	blood:	n/a	n/a
11	MYC	chr2:234620209-234620261	HepG2	liver:	n/a	n/a
12	CTCF	chr2:234620180-234620330	HMEC	breast:	n/a	chr2:234620245-234620261 chr2:234620246-234620259 chr2:234620246-234620259 chr2:234620244-234620262 chr2:234620239-234620260 chr2:234620247-234620257 chr2:234620250-234620259
13	CTCF	chr2:234620200-234620350	GM12870	blood:	n/a	chr2:234620245-234620261 chr2:234620246-234620259 chr2:234620246-234620259 chr2:234620244-234620262 chr2:234620239-234620260 chr2:234620247-234620257 chr2:234620250-234620259
14	CEBPB	chr2:234620072-234620388	Hela-S3	cervix:	n/a	n/a
15	REST	chr2:234620051-234620363	SK-N-SH	brain:	n/a	chr2:234620258-234620267
16	CTCF	chr2:234620180-234620330	HUVEC	blood vessel:	n/a	chr2:234620245-234620261 chr2:234620246-234620259 chr2:234620246-234620259 chr2:234620244-234620262 chr2:234620239-234620260 chr2:234620247-234620257 chr2:234620250-234620259
17	CTCF	chr2:234620180-234620330	HCT-116	colon:	n/a	chr2:234620245-234620261 chr2:234620246-234620259 chr2:234620246-234620259 chr2:234620244-234620262 chr2:234620239-234620260 chr2:234620247-234620257 chr2:234620250-234620259
18	CTCF	chr2:234620220-234620370	BJ	skin:	n/a	chr2:234620245-234620261 chr2:234620246-234620259 chr2:234620246-234620259 chr2:234620244-234620262 chr2:234620239-234620260 chr2:234620247-234620257 chr2:234620250-234620259
19	CTCF	chr2:234620108-234620567	GM19239	blood:	n/a	chr2:234620245-234620261 chr2:234620246-234620259 chr2:234620246-234620259 chr2:234620244-234620262 chr2:234620239-234620260 chr2:234620247-234620257 chr2:234620250-234620259
20	CTCF	chr2:234620127-234620393	Pancreas_OC	pancreas:	n/a	chr2:234620245-234620261 chr2:234620246-234620259 chr2:234620246-234620259 chr2:234620244-234620262 chr2:234620239-234620260 chr2:234620247-234620257 chr2:234620250-234620259
21	YY1	chr2:234620066-234620435	GM12892	blood:	n/a	chr2:234620242-234620256
22	CTCF	chr2:234620120-234620270	HepG2	liver:	n/a	chr2:234620245-234620261 chr2:234620246-234620259 chr2:234620246-234620259 chr2:234620244-234620262 chr2:234620239-234620260 chr2:234620247-234620257 chr2:234620250-234620259
23	CTCF	chr2:234620120-234620270	SAEC	small airway:	n/a	chr2:234620245-234620261 chr2:234620246-234620259 chr2:234620246-234620259 chr2:234620244-234620262 chr2:234620239-234620260 chr2:234620247-234620257 chr2:234620250-234620259
24	CTCF	chr2:234620160-234620310	BJ	skin:	n/a	chr2:234620245-234620261 chr2:234620246-234620259 chr2:234620246-234620259 chr2:234620244-234620262 chr2:234620239-234620260 chr2:234620247-234620257 chr2:234620250-234620259
25	CTCF	chr2:234620180-234620330	HPF	lung:	n/a	chr2:234620245-234620261 chr2:234620246-234620259 chr2:234620246-234620259 chr2:234620244-234620262 chr2:234620239-234620260 chr2:234620247-234620257 chr2:234620250-234620259
26	CTCF	chr2:234620200-234620350	GM12868	blood:	n/a	chr2:234620245-234620261 chr2:234620246-234620259 chr2:234620246-234620259 chr2:234620244-234620262 chr2:234620239-234620260 chr2:234620247-234620257 chr2:234620250-234620259
27	FOSL2	chr2:234619971-234620598	A549	lung:	n/a	n/a
28	CTCF	chr2:234620180-234620330	AG09319	gingival:	n/a	chr2:234620245-234620261 chr2:234620246-234620259 chr2:234620246-234620259 chr2:234620244-234620262 chr2:234620239-234620260 chr2:234620247-234620257 chr2:234620250-234620259
29	CTCF	chr2:234620113-234620402	H1-hESC	embryonic stem cell:	n/a	chr2:234620245-234620261 chr2:234620246-234620259 chr2:234620246-234620259 chr2:234620244-234620262 chr2:234620239-234620260 chr2:234620247-234620257 chr2:234620250-234620259
30	CTCF	chr2:234620120-234620270	HFF-Myc	foreskin:	n/a	chr2:234620245-234620261 chr2:234620246-234620259 chr2:234620246-234620259 chr2:234620244-234620262 chr2:234620239-234620260 chr2:234620247-234620257 chr2:234620250-234620259
31	CTCF	chr2:234620142-234620373	SK-N-SH_RA	brain:	n/a	chr2:234620245-234620261 chr2:234620246-234620259 chr2:234620246-234620259 chr2:234620244-234620262 chr2:234620239-234620260 chr2:234620247-234620257 chr2:234620250-234620259
32	CTCF	chr2:234620180-234620330	HCPEpiC	choroid plexus:	n/a	chr2:234620245-234620261 chr2:234620246-234620259 chr2:234620246-234620259 chr2:234620244-234620262 chr2:234620239-234620260 chr2:234620247-234620257 chr2:234620250-234620259
33	CTCF	chr2:234620180-234620330	Caco-2	colon:	n/a	chr2:234620245-234620261 chr2:234620246-234620259 chr2:234620246-234620259 chr2:234620244-234620262 chr2:234620239-234620260 chr2:234620247-234620257 chr2:234620250-234620259
34	ZNF143	chr2:234620110-234620426	H1-hESC	embryonic stem cell:	n/a	n/a
35	SP1	chr2:234619759-234620586	A549	lung:	n/a	n/a
36	CTCF	chr2:234620200-234620350	HL-60	blood:	n/a	chr2:234620245-234620261 chr2:234620246-234620259 chr2:234620246-234620259 chr2:234620244-234620262 chr2:234620239-234620260 chr2:234620247-234620257 chr2:234620250-234620259
37	CTCF	chr2:234620180-234620330	AG09309	skin:	n/a	chr2:234620245-234620261 chr2:234620246-234620259 chr2:234620246-234620259 chr2:234620244-234620262 chr2:234620239-234620260 chr2:234620247-234620257 chr2:234620250-234620259
38	CTCF	chr2:234620140-234620290	HFF	foreskin:	n/a	chr2:234620245-234620261 chr2:234620246-234620259 chr2:234620246-234620259 chr2:234620244-234620262 chr2:234620239-234620260 chr2:234620247-234620257 chr2:234620250-234620259
39	RFX5	chr2:234620084-234620370	Hela-S3	cervix:	n/a	n/a
40	STAT3	chr2:234620207-234620370	MCF10A-Er-Src	breast:	n/a	chr2:234620341-234620349 chr2:234620271-234620283 chr2:234620237-234620245
41	CTCF	chr2:234620200-234620350	NB4	blood:	n/a	chr2:234620245-234620261 chr2:234620246-234620259 chr2:234620246-234620259 chr2:234620244-234620262 chr2:234620239-234620260 chr2:234620247-234620257 chr2:234620250-234620259
42	YY1	chr2:234620064-234620427	GM12878	blood:	n/a	chr2:234620242-234620256
43	CTCF	chr2:234620160-234620310	AG04449	skin:	n/a	chr2:234620245-234620261 chr2:234620246-234620259 chr2:234620246-234620259 chr2:234620244-234620262 chr2:234620239-234620260 chr2:234620247-234620257 chr2:234620250-234620259
44	CTCF	chr2:234620200-234620350	SAEC	small airway:	n/a	chr2:234620245-234620261 chr2:234620246-234620259 chr2:234620246-234620259 chr2:234620244-234620262 chr2:234620239-234620260 chr2:234620247-234620257 chr2:234620250-234620259
45	CTCF	chr2:234620200-234620350	HPAF	blood vessel:	n/a	chr2:234620245-234620261 chr2:234620246-234620259 chr2:234620246-234620259 chr2:234620244-234620262 chr2:234620239-234620260 chr2:234620247-234620257 chr2:234620250-234620259
46	CTCF	chr2:234620180-234620330	MCF-7	breast:	n/a	chr2:234620245-234620261 chr2:234620246-234620259 chr2:234620246-234620259 chr2:234620244-234620262 chr2:234620239-234620260 chr2:234620247-234620257 chr2:234620250-234620259
47	CTCF	chr2:234620160-234620310	HEK293	kidney:	n/a	chr2:234620245-234620261 chr2:234620246-234620259 chr2:234620246-234620259 chr2:234620244-234620262 chr2:234620239-234620260 chr2:234620247-234620257 chr2:234620250-234620259
48	CTCF	chr2:234620220-234620370	GM12878	blood:	n/a	chr2:234620245-234620261 chr2:234620246-234620259 chr2:234620246-234620259 chr2:234620244-234620262 chr2:234620239-234620260 chr2:234620247-234620257 chr2:234620250-234620259
49	FOS	chr2:234620213-234620307	MCF10A-Er-Src	breast:	n/a	n/a
50	CTCF	chr2:234620180-234620330	GM12873	blood:	n/a	chr2:234620245-234620261 chr2:234620246-234620259 chr2:234620246-234620259 chr2:234620244-234620262 chr2:234620239-234620260 chr2:234620247-234620257 chr2:234620250-234620259

No.	Distal block	Cell Line	Cell type
1	chr2:234474046..234476375-chr2:234618981..234621894,3	MCF-7	breast:
2	chr2:234389181..234390135-chr2:234619766..234620786,6	MCF-7	breast:
3	chr2:234386983..234399433-chr2:234613282..234621553,23	MCF-7	breast:
4	chr2:234613252..234614909-chr2:234617932..234620320,3	MCF-7	breast:
5	chr2:234599124..234606471-chr2:234613478..234621007,17	MCF-7	breast:
6	chr2:234357834..234358362-chr2:234619860..234620685,2	MCF-7	breast:
7	chr2:234393460..234398388-chr2:234612624..234620814,16	MCF-7	breast:
8	chr2:234356803..234357518-chr2:234620184..234620760,2	MCF-7	breast:
9	chr2:234366581..234368147-chr2:234619420..234621425,2	MCF-7	breast:

Variant related genes	Relation type
UGT1A8	TF binding region
UGT1A5	TF binding region
ENSG00000224814	TF binding region
ENSG00000167165	Chromatin interaction
ENSG00000077044	Chromatin interaction
ENSG00000085982	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs28898599	1.00[AFR][1000 genomes]
rs28898604	1.00[AFR][1000 genomes]
rs28898613	1.00[AFR][1000 genomes]
rs28899174	0.93[AFR][1000 genomes]
rs45470199	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv428072	chr2:234393609-234624769	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1010936	chr2:234549011-234640221	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	esv2760615	chr2:234613030-234640233	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv963781	chr2:234618109-234626863	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
8	nsv876017	chr2:234618243-234626972	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234615400-234620400	Weak transcription	Pancreas	Pancrea
2	chr2:234617800-234620400	Weak transcription	Esophagus	oesophagus
3	chr2:234617800-234631600	Weak transcription	Gastric	stomach
4	chr2:234618600-234621400	Enhancers	Liver	Liver
5	chr2:234618800-234620400	Enhancers	Hela-S3	cervix
6	chr2:234619600-234620400	Genic enhancers	NHEK	skin
7	chr2:234619600-234620600	Enhancers	Stomach Mucosa	stomach
8	chr2:234619800-234620400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:234619800-234620600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:234619800-234620600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:234619800-234623000	Enhancers	Thymus	Thymus
12	chr2:234620000-234620400	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr2:234620000-234620600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:234620000-234621200	Enhancers	Duodenum Mucosa	Duodenum
15	chr2:234620000-234621400	Enhancers	Small Intestine	intestine
16	chr2:234620000-234621400	Enhancers	A549	lung
17	chr2:234620000-234622200	Enhancers	Fetal Intestine Large	intestine
18	chr2:234620200-234622200	Enhancers	Fetal Intestine Small	intestine

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