Variant report

Variant	rs17009396
Chromosome Location	chr2:74054272-74054273
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:131)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:131 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr2:74054233-74054354	SK-N-SH_RA	brain:	n/a	n/a
2	CTCF	chr2:74054240-74054390	BJ	skin:	n/a	n/a
3	CTCF	chr2:74054220-74054370	SAEC	small airway:	n/a	n/a
4	RAD21	chr2:74054168-74054474	HepG2	liver:	n/a	n/a
5	RAD21	chr2:74054188-74054580	ECC-1	luminal epithelium:	n/a	n/a
6	CTCF	chr2:74054220-74054370	GM12866	blood:	n/a	n/a
7	CTCF	chr2:74054260-74054410	HFF-Myc	foreskin:	n/a	n/a
8	CTCF	chr2:74054260-74054410	RPTEC	kidney:	n/a	n/a
9	CTCF	chr2:74054180-74054330	HCM	heart:	n/a	n/a
10	CTCF	chr2:74054236-74054396	Hela-S3	cervix:	n/a	n/a
11	CTCF	chr2:74054165-74054525	HCT-116	colon:	n/a	n/a
12	SMC3	chr2:74054158-74054493	HepG2	liver:	n/a	n/a
13	CTCF	chr2:74054240-74054390	HCFaa	heart:	n/a	n/a
14	CTCF	chr2:74054017-74054703	HCT-116	colon:	n/a	chr2:74054555-74054563
15	RAD21	chr2:74054158-74054486	IMR90	lung:	n/a	n/a
16	RAD21	chr2:74054210-74054407	HepG2	liver:	n/a	n/a
17	FOXA2	chr2:74054229-74054396	HepG2	liver:	n/a	n/a
18	CTCF	chr2:74054220-74054370	HVMF	connective:	n/a	n/a
19	CTCF	chr2:74054224-74054405	GM10266	blood:	n/a	n/a
20	CTCF	chr2:74054260-74054410	AG04449	skin:	n/a	n/a
21	CTCF	chr2:74054235-74054385	GM10248	blood:	n/a	n/a
22	CTCF	chr2:74054200-74054350	GM12872	blood:	n/a	n/a
23	CTCF	chr2:74054220-74054370	WERI-Rb-1	eye:	n/a	n/a
24	CTCF	chr2:74054220-74054370	HMF	breast:	n/a	n/a
25	CTCF	chr2:74054200-74054350	NHEK	skin:	n/a	n/a
26	CTCF	chr2:74054260-74054410	GM06990	blood:	n/a	n/a
27	CTCF	chr2:74054260-74054410	HUVEC	blood vessel:	n/a	n/a
28	CTCF	chr2:74054240-74054390	HCPEpiC	choroid plexus:	n/a	n/a
29	CTCF	chr2:74054240-74054390	GM12865	blood:	n/a	n/a
30	CTCF	chr2:74054255-74054376	MCF-7	breast:	n/a	n/a
31	CTCF	chr2:74054220-74054370	HRE	kidney:	n/a	n/a
32	ZMIZ1	chr2:74054145-74054375	K562	blood:	n/a	n/a
33	CTCF	chr2:74054240-74054390	HEK293	kidney:	n/a	n/a
34	CTCF	chr2:74054240-74054390	GM12864	blood:	n/a	n/a
35	CTCF	chr2:74054237-74054400	HepG2	liver:	n/a	n/a
36	CTCF	chr2:74054217-74054426	K562	blood:	n/a	n/a
37	CTCF	chr2:74054200-74054452	HUVEC	blood vessel:	n/a	n/a
38	CTCF	chr2:74054260-74054410	HCPEpiC	choroid plexus:	n/a	n/a
39	CTCF	chr2:74054105-74055554	A549	lung:	n/a	chr2:74054555-74054563
40	CTCF	chr2:74054240-74054390	BE2_C	brain:	n/a	n/a
41	SMC3	chr2:74054156-74054474	GM12878	blood:	n/a	n/a
42	CTCF	chr2:74054129-74054503	GM12878	blood:	n/a	n/a
43	CTCF	chr2:74054240-74054390	HCT-116	colon:	n/a	n/a
44	CTCF	chr2:74054220-74054370	Hela-S3	cervix:	n/a	n/a
45	CTCF	chr2:74054220-74054370	AG04450	lung:	n/a	n/a
46	CTCF	chr2:74054240-74054390	GM06990	blood:	n/a	n/a
47	CTCF	chr2:74054240-74054390	HepG2	liver:	n/a	n/a
48	CTCF	chr2:74054106-74054521	HepG2	liver:	n/a	n/a
49	ATF1	chr2:74054225-74054417	K562	blood:	n/a	n/a
50	CTCF	chr2:74054220-74054370	HUVEC	blood vessel:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:74004444..74006020-chr2:74053313..74055286,2	K562	blood:
2	chr2:74053720..74055636-chr2:74377431..74379378,2	MCF-7	breast:
3	chr2:73962060..73965748-chr2:74053469..74057980,4	K562	blood:
4	chr2:74006977..74007746-chr2:74053873..74054726,2	MCF-7	breast:
5	chr2:74004444..74007409-chr2:74053786..74057952,3	K562	blood:
6	chr2:74054272..74058005-chr2:74424584..74427795,4	K562	blood:
7	chr2:74052797..74060455-chr2:74207744..74214705,21	MCF-7	breast:
8	chr2:74053154..74055728-chr2:74152943..74154610,2	MCF-7	breast:

No data

Variant related genes	Relation type
STAMBP	TF binding region
ENSG00000144048	Chromatin interaction
ENSG00000144034	Chromatin interaction
ENSG00000237883	Chromatin interaction
ENSG00000065911	Chromatin interaction
ENSG00000235499	Chromatin interaction
ENSG00000114956	Chromatin interaction
ENSG00000255989	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10167667	0.88[ASN][1000 genomes]
rs10202343	0.88[ASN][1000 genomes]
rs1055888	0.88[ASN][1000 genomes]
rs11126419	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11890369	1.00[GIH][hapmap];0.82[MEX][hapmap]
rs11897051	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12614068	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12618950	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12623504	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13012471	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13414927	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs13418993	0.88[ASN][1000 genomes]
rs13419314	0.88[ASN][1000 genomes]
rs13432600	0.88[ASN][1000 genomes]
rs17009399	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17009404	1.00[CHB][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3738845	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3813230	0.81[CHD][hapmap]
rs3813233	1.00[GIH][hapmap]
rs56665235	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56875063	0.85[ASN][1000 genomes]
rs58787134	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59974236	0.85[ASN][1000 genomes]
rs60987687	0.88[ASN][1000 genomes]
rs61314551	0.85[ASN][1000 genomes]
rs6705766	1.00[GIH][hapmap];0.82[MEX][hapmap]
rs72915479	0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72917405	0.88[ASN][1000 genomes]
rs72917409	0.91[ASN][1000 genomes]
rs72917413	0.91[ASN][1000 genomes]
rs72917415	0.88[ASN][1000 genomes]
rs72917417	0.88[ASN][1000 genomes]
rs72917422	0.88[ASN][1000 genomes]
rs7572565	1.00[ASN][1000 genomes]
rs7579755	0.88[ASN][1000 genomes]
rs7581248	1.00[GIH][hapmap]
rs7592693	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7609273	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs919629	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757806	chr2:73717032-74078592	Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer 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	36 gene(s)	inside rSNPs	diseases
2	esv2759060	chr2:73717032-74078592	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv834260	chr2:73906106-74076520	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv2780	chr2:73994168-74057248	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74048800-74054800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr2:74050000-74054800	Weak transcription	Primary B cells from peripheral blood	blood
3	chr2:74050800-74054600	Weak transcription	GM12878-XiMat	blood
4	chr2:74051600-74054600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:74051800-74055200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr2:74051800-74055200	Weak transcription	Adipose Nuclei	Adipose
7	chr2:74053000-74055400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:74053800-74055400	Enhancers	Rectal Smooth Muscle	rectum
9	chr2:74053800-74055400	Enhancers	Stomach Smooth Muscle	stomach

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