Variant report

Variant	rs28898595
Chromosome Location	chr2:234620533-234620534
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	chr2:234620108-234620567	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
2	FOSL2	chr2:234619971-234620598	A549	lung:	n/a	n/a
3	SP1	chr2:234619759-234620586	A549	lung:	n/a	n/a
4	TCF12	chr2:234618903-234620639	A549	lung:	n/a	chr2:234620027-234620034
5	CTCF	chr2:234620092-234620571	GM12891	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	RAD21	chr2:234619910-234620545	H1-hESC	embryonic stem cell:	n/a	chr2:234620248-234620257 chr2:234620242-234620261 chr2:234620244-234620256
7	CTCF	chr2:234620494-234620618	GM12878	blood:	n/a	n/a
8	EP300	chr2:234619708-234620620	A549	lung:	n/a	chr2:234620402-234620416 chr2:234620430-234620446
9	CTCF	chr2:234620030-234620565	K562	blood:	n/a	chr2:234620245-234620261 chr2:234620246-234620259 chr2:234620246-234620259 chr2:234620244-234620262 chr2:234620239-234620260 chr2:234620247-234620257 chr2:234620250-234620259
10	MAX	chr2:234619991-234620672	A549	lung:	n/a	n/a
11	RAD21	chr2:234619826-234620610	SK-N-SH	brain:	n/a	chr2:234620248-234620257 chr2:234620242-234620261 chr2:234620244-234620256
12	CTCF	chr2:234620088-234620583	GM12892	blood:	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	chr2:234620075-234620573	GM19238	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	CTCF	chr2:234620526-234620551	GM20000	blood:	n/a	n/a
15	POLR2A	chr2:234620484-234620582	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTCF	chr2:234620082-234620596	GM19240	blood:	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	chr2:234619924-234620646	SK-N-SH	brain:	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	chr2:234618797-234620924	A549	lung:	n/a	chr2:234620245-234620261 chr2:234620246-234620259 chr2:234620246-234620259 chr2:234620244-234620262 chr2:234620239-234620260 chr2:234620247-234620257 chr2:234620250-234620259
19	SP1	chr2:234619811-234620542	A549	lung:	n/a	n/a
20	CTCF	chr2:234619933-234620551	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
21	SMC3	chr2:234619782-234620633	SK-N-SH	brain:	n/a	chr2:234620246-234620260
22	BCL3	chr2:234619957-234620684	A549	lung:	n/a	chr2:234620657-234620664 chr2:234620407-234620416
23	MAZ	chr2:234620066-234620555	IMR90	lung:	n/a	n/a
24	MAX	chr2:234619563-234620672	A549	lung:	n/a	n/a
25	RAD21	chr2:234619902-234620616	HCT-116	colon:	n/a	chr2:234620248-234620257 chr2:234620242-234620261 chr2:234620244-234620256
26	ZNF263	chr2:234619653-234620533	HEK293-T-REx	kidney:	n/a	chr2:234620340-234620349
27	REST	chr2:234619948-234620563	A549	lung:	n/a	chr2:234620258-234620267
28	CTCF	chr2:234620019-234620549	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
29	RAD21	chr2:234619998-234620544	ECC-1	luminal epithelium:	n/a	chr2:234620248-234620257 chr2:234620242-234620261 chr2:234620244-234620256
30	RAD21	chr2:234619823-234620662	A549	lung:	n/a	chr2:234620248-234620257 chr2:234620242-234620261 chr2:234620244-234620256
31	RAD21	chr2:234619946-234620556	HepG2	liver:	n/a	chr2:234620248-234620257 chr2:234620242-234620261 chr2:234620244-234620256
32	CTCF	chr2:234620507-234620614	GM10266	blood:	n/a	n/a

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	chr2:234599124..234606471-chr2:234613478..234621007,17	MCF-7	breast:
5	chr2:234357834..234358362-chr2:234619860..234620685,2	MCF-7	breast:
6	chr2:234393460..234398388-chr2:234612624..234620814,16	MCF-7	breast:
7	chr2:234356803..234357518-chr2:234620184..234620760,2	MCF-7	breast:
8	chr2:234366581..234368147-chr2:234619420..234621425,2	MCF-7	breast:

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

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1018124	0.93[ASN][1000 genomes]
rs10929293	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12052787	0.93[ASN][1000 genomes]
rs12463641	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12463910	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12466747	0.85[ASN][1000 genomes]
rs12466779	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12466997	0.93[ASN][1000 genomes]
rs12468274	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12468356	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12468543	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12474980	0.81[ASN][1000 genomes]
rs12475068	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12475934	0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12476197	0.82[ASN][1000 genomes]
rs12477216	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12479045	0.94[ASN][1000 genomes]
rs12479208	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17862867	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17862868	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs17862869	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs17862870	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17862871	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17862872	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17862878	0.94[ASN][1000 genomes]
rs17863790	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17863791	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17863798	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17864686	0.80[ASN][1000 genomes]
rs17864696	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17864697	0.94[ASN][1000 genomes]
rs17864705	0.94[ASN][1000 genomes]
rs17868325	0.80[ASN][1000 genomes]
rs17868333	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17868334	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17868335	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17874943	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003569	0.93[ASN][1000 genomes]
rs2011219	0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2011425	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2012736	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2013018	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2013021	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2013030	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2885295	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28898596	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28898605	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28898615	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs28898621	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28899186	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs28899187	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs28899189	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28899191	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3732217	0.83[ASN][1000 genomes]
rs3732218	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732219	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732220	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732221	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755320	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755321	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755322	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755323	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3771342	0.94[ASN][1000 genomes]
rs3796088	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3806591	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806593	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806594	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806595	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3892170	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3893334	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4485562	0.80[ASN][1000 genomes]
rs4556969	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4663325	0.88[EUR][1000 genomes]
rs4663326	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4663327	0.88[EUR][1000 genomes]
rs4663945	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4663964	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4663966	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4663968	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs5020121	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62191898	0.88[EUR][1000 genomes]
rs62191916	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs62191917	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs62191918	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6753317	0.80[ASN][1000 genomes]
rs7420193	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs904855	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs904856	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[ASN][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:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234617800-234631600	Weak transcription	Gastric	stomach
2	chr2:234618600-234621400	Enhancers	Liver	Liver
3	chr2:234619600-234620600	Enhancers	Stomach Mucosa	stomach
4	chr2:234619800-234620600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:234619800-234620600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:234619800-234623000	Enhancers	Thymus	Thymus
7	chr2:234620000-234620600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:234620000-234621200	Enhancers	Duodenum Mucosa	Duodenum
9	chr2:234620000-234621400	Enhancers	Small Intestine	intestine
10	chr2:234620000-234621400	Enhancers	A549	lung
11	chr2:234620000-234622200	Enhancers	Fetal Intestine Large	intestine
12	chr2:234620200-234622200	Enhancers	Fetal Intestine Small	intestine
13	chr2:234620400-234620600	Enhancers	Esophagus	oesophagus
14	chr2:234620400-234620600	Enhancers	Pancreas	Pancrea
15	chr2:234620400-234620800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:234620400-234622200	Strong transcription	NHEK	skin
17	chr2:234620400-234659200	Weak transcription	Colonic Mucosa	Colon

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