Variant report

Variant	rs6715989
Chromosome Location	chr2:98912271-98912272
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:51)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:51 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr2:98912209-98912537	IMR90	lung:	n/a	n/a
2	RAD21	chr2:98912238-98912476	H1-hESC	embryonic stem cell:	n/a	n/a
3	RAD21	chr2:98912214-98912463	SK-N-SH_RA	brain:	n/a	n/a
4	RAD21	chr2:98912269-98912474	K562	blood:	n/a	n/a
5	RAD21	chr2:98912214-98912482	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr2:98912260-98912410	Hela-S3	cervix:	n/a	n/a
7	CTCF	chr2:98912220-98912370	HA-sp	spinal cord:	n/a	n/a
8	RAD21	chr2:98912216-98912458	SK-N-SH_RA	brain:	n/a	n/a
9	CTCF	chr2:98912260-98912410	K562	blood:	n/a	n/a
10	CTCF	chr2:98912261-98912446	MCF-7	breast:	n/a	n/a
11	CTCF	chr2:98912209-98912526	K562	blood:	n/a	n/a
12	CTCF	chr2:98912180-98912470	AG04450	lung:	n/a	n/a
13	CTCF	chr2:98912260-98912410	HPAF	blood vessel:	n/a	n/a
14	CTCF	chr2:98912266-98912441	MCF-7	breast:	n/a	n/a
15	RAD21	chr2:98912262-98912553	HepG2	liver:	n/a	n/a
16	CTCF	chr2:98912180-98912330	A549	lung:	n/a	n/a
17	CTCF	chr2:98912130-98912512	HepG2	liver:	n/a	n/a
18	CTCF	chr2:98912260-98912446	Gliobla	brain:	n/a	n/a
19	CTCF	chr2:98912200-98912460	K562	blood:	n/a	n/a
20	RAD21	chr2:98912222-98912511	A549	lung:	n/a	n/a
21	CTCF	chr2:98912220-98912370	GM12864	blood:	n/a	n/a
22	CTCF	chr2:98912262-98912445	MCF-7	breast:	n/a	n/a
23	CTCF	chr2:98912149-98912457	A549	lung:	n/a	n/a
24	CTCF	chr2:98912199-98912495	K562	blood:	n/a	n/a
25	RAD21	chr2:98912184-98912584	H1-hESC	embryonic stem cell:	n/a	n/a
26	RAD21	chr2:98912124-98912632	A549	lung:	n/a	n/a
27	CTCF	chr2:98912157-98912523	A549	lung:	n/a	n/a
28	CTCF	chr2:98912221-98912463	HepG2	liver:	n/a	n/a
29	CTCF	chr2:98912140-98912430	HFF-Myc	foreskin:	n/a	n/a
30	RAD21	chr2:98912225-98912628	MCF-7	breast:	n/a	n/a
31	CTCF	chr2:98912261-98912467	K562	blood:	n/a	n/a
32	CTCF	chr2:98912260-98912410	WERI-Rb-1	eye:	n/a	n/a
33	RAD21	chr2:98912265-98912414	K562	blood:	n/a	n/a
34	CTCF	chr2:98912200-98912350	BE2_C	brain:	n/a	n/a
35	RAD21	chr2:98912162-98912450	HepG2	liver:	n/a	n/a
36	CTCF	chr2:98912260-98912410	AG09309	skin:	n/a	n/a
37	CTCF	chr2:98912200-98912350	AoAF	blood vessel:	n/a	n/a
38	RAD21	chr2:98912129-98912611	HepG2	liver:	n/a	n/a
39	CTCF	chr2:98912219-98912511	GM12878	blood:	n/a	n/a
40	CTCF	chr2:98912240-98912390	RPTEC	kidney:	n/a	n/a
41	CTCF	chr2:98912260-98912410	GM12866	blood:	n/a	n/a
42	CTCF	chr2:98912200-98912350	HBMEC	blood vessel:	n/a	n/a
43	CTCF	chr2:98912260-98912410	SAEC	small airway:	n/a	n/a
44	CTCF	chr2:98912260-98912410	WI-38	lung:	n/a	n/a
45	CTCF	chr2:98912240-98912390	Hela-S3	cervix:	n/a	n/a
46	CTCF	chr2:98912200-98912350	GM12872	blood:	n/a	n/a
47	RAD21	chr2:98912222-98912481	ECC-1	luminal epithelium:	n/a	n/a
48	RAD21	chr2:98912243-98912659	MCF-7	breast:	n/a	n/a
49	CTCF	chr2:98912260-98912410	HMF	breast:	n/a	n/a
50	RAD21	chr2:98912153-98912612	A549	lung:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:98911862..98912813-chr2:99001255..99002233,2	K562	blood:
2	chr2:98912225..98912826-chr2:99185396..99186137,2	MCF-7	breast:
3	chr2:98910828..98912979-chr2:98930336..98932005,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000216112	TF binding region

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10176056	1.00[ASN][1000 genomes]
rs10181000	0.87[CHB][hapmap]
rs10190336	0.84[ASN][1000 genomes]
rs10199476	1.00[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap]
rs10201994	1.00[ASN][1000 genomes]
rs10202618	0.98[ASN][1000 genomes]
rs10203437	0.98[ASN][1000 genomes]
rs11124096	1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap]
rs11124107	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs11124121	0.87[ASN][1000 genomes]
rs11673807	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs11679920	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs11889349	1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs11891512	0.82[ASN][1000 genomes]
rs11895654	1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap]
rs11901562	0.92[ASN][1000 genomes]
rs12478763	1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs12478769	0.82[ASN][1000 genomes]
rs12622324	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs12624294	1.00[ASN][1000 genomes]
rs12712256	0.92[ASN][1000 genomes]
rs12993718	0.82[ASN][1000 genomes]
rs12999985	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs13013876	0.82[ASN][1000 genomes]
rs13014142	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs13033263	0.82[ASN][1000 genomes]
rs13394706	0.87[CHB][hapmap]
rs13408372	0.85[CHB][hapmap]
rs13415414	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13428221	0.83[ASN][1000 genomes]
rs1451251	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs1466944	1.00[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs1504679	0.98[ASN][1000 genomes]
rs17427684	0.98[ASN][1000 genomes]
rs17428056	1.00[ASN][1000 genomes]
rs17429208	0.87[CHB][hapmap]
rs17493655	1.00[ASN][1000 genomes]
rs17493788	1.00[ASN][1000 genomes]
rs1875880	0.98[ASN][1000 genomes]
rs2102270	0.87[CHB][hapmap];0.82[MEX][hapmap]
rs2122756	1.00[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap]
rs2202387	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2221416	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2292118	0.87[CHB][hapmap]
rs2292119	1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap]
rs3731659	0.98[ASN][1000 genomes]
rs4374424	1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs4389366	0.92[ASN][1000 genomes]
rs4455212	1.00[CHB][hapmap]
rs4477970	1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs4479470	1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs4494805	0.82[ASN][1000 genomes]
rs4535095	0.81[ASN][1000 genomes]
rs4608580	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4632400	1.00[CHB][hapmap];0.82[CHD][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs4851122	0.92[ASN][1000 genomes]
rs4851123	0.98[ASN][1000 genomes]
rs4851124	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4851935	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs4851951	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs4851952	0.82[ASN][1000 genomes]
rs4851954	0.94[ASN][1000 genomes]
rs4851955	0.98[ASN][1000 genomes]
rs4851959	0.98[ASN][1000 genomes]
rs4851960	0.91[ASN][1000 genomes]
rs56320609	0.84[AMR][1000 genomes]
rs62157914	1.00[ASN][1000 genomes]
rs6543419	1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs6543459	1.00[ASN][1000 genomes]
rs66464436	1.00[ASN][1000 genomes]
rs6725543	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[ASN][1000 genomes]
rs6742930	0.98[ASN][1000 genomes]
rs6747344	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs6747410	0.87[CHB][hapmap];0.81[CHD][hapmap]
rs6750975	0.98[ASN][1000 genomes]
rs6754222	0.81[CHB][hapmap]
rs72933220	1.00[ASN][1000 genomes]
rs7571001	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7572757	1.00[ASN][1000 genomes]
rs7574218	0.82[ASN][1000 genomes]
rs7578802	1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs7580008	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7589018	1.00[ASN][1000 genomes]
rs7598554	0.92[ASN][1000 genomes]
rs7601049	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs7606070	0.98[ASN][1000 genomes]
rs7606220	1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap]
rs937726	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1004082	chr2:98792256-98967681	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv535833	chr2:98792256-98967681	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6715989	ANKRD39	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98898800-98913200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:98905000-98915600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:98910200-98913200	Enhancers	Stomach Mucosa	stomach
4	chr2:98911200-98913200	Enhancers	Adipose Nuclei	Adipose
5	chr2:98911400-98912800	Flanking Bivalent TSS/Enh	HepG2	liver
6	chr2:98911600-98912800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr2:98911600-98913000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr2:98911600-98915800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:98911600-98916400	Weak transcription	Brain Anterior Caudate	brain
10	chr2:98911800-98912600	Enhancers	HUVEC	blood vessel
11	chr2:98912000-98912800	Enhancers	Liver	Liver
12	chr2:98912000-98913200	Enhancers	Gastric	stomach
13	chr2:98912000-98916400	Weak transcription	Brain Hippocampus Middle	brain
14	chr2:98912200-98912800	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr2:98912200-98913200	Enhancers	Pancreas	Pancrea
16	chr2:98912200-98915800	Weak transcription	Brain Angular Gyrus	brain
17	chr2:98912200-98915800	Weak transcription	Brain Cingulate Gyrus	brain

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