Variant report

Variant	rs2041868
Chromosome Location	chr2:50756800-50756801
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	chr2:50756689-50757192	SK-N-SH	brain:	n/a	chr2:50756940-50756958 chr2:50756945-50756953 chr2:50756942-50756963
2	RAD21	chr2:50756723-50757116	H1-hESC	embryonic stem cell:	n/a	chr2:50756941-50756960
3	RAD21	chr2:50756795-50757050	A549	lung:	n/a	chr2:50756941-50756960
4	RAD21	chr2:50756748-50756997	GM12878	blood:	n/a	chr2:50756941-50756960
5	CTCF	chr2:50756760-50757063	GM12878	blood:	n/a	chr2:50756940-50756958 chr2:50756945-50756953 chr2:50756942-50756963
6	RAD21	chr2:50756779-50757121	HepG2	liver:	n/a	chr2:50756941-50756960
7	CTCF	chr2:50756721-50757289	GM12878	blood:	n/a	chr2:50756940-50756958 chr2:50756945-50756953 chr2:50756942-50756963
8	CTCF	chr2:50756721-50757117	HepG2	liver:	n/a	chr2:50756940-50756958 chr2:50756945-50756953 chr2:50756942-50756963
9	RAD21	chr2:50756659-50757219	HCT-116	colon:	n/a	chr2:50756941-50756960
10	RAD21	chr2:50756793-50757150	ECC-1	luminal epithelium:	n/a	chr2:50756941-50756960
11	SMC3	chr2:50756767-50757135	GM12878	blood:	n/a	n/a
12	CTCF	chr2:50756796-50757081	HUVEC	blood vessel:	n/a	chr2:50756940-50756958 chr2:50756945-50756953 chr2:50756942-50756963
13	BRCA1	chr2:50756704-50757012	H1-hESC	embryonic stem cell:	n/a	n/a
14	CTCF	chr2:50756780-50756930	GM12867	blood:	n/a	n/a
15	CTCF	chr2:50756760-50756910	WI-38	lung:	n/a	n/a
16	CTCF	chr2:50756794-50757015	HepG2	liver:	n/a	chr2:50756940-50756958 chr2:50756945-50756953 chr2:50756942-50756963
17	ARID3A	chr2:50756786-50757088	HepG2	liver:	n/a	chr2:50757036-50757052 chr2:50757037-50757053
18	RAD21	chr2:50756663-50757207	HepG2	liver:	n/a	chr2:50756941-50756960
19	RAD21	chr2:50756715-50757169	H1-hESC	embryonic stem cell:	n/a	chr2:50756941-50756960
20	RAD21	chr2:50756313-50757267	SK-N-SH	brain:	n/a	chr2:50756941-50756960
21	CTCF	chr2:50756747-50757129	IMR90	lung:	n/a	chr2:50756940-50756958 chr2:50756945-50756953 chr2:50756942-50756963
22	RAD21	chr2:50756778-50757008	HepG2	liver:	n/a	chr2:50756941-50756960
23	CTCF	chr2:50756730-50757043	GM10248	blood:	n/a	chr2:50756940-50756958 chr2:50756945-50756953 chr2:50756942-50756963
24	RAD21	chr2:50756707-50757209	HCT-116	colon:	n/a	chr2:50756941-50756960
25	RAD21	chr2:50756726-50757220	A549	lung:	n/a	chr2:50756941-50756960
26	CTCF	chr2:50756742-50757130	A549	lung:	n/a	chr2:50756940-50756958 chr2:50756945-50756953 chr2:50756942-50756963
27	CTCF	chr2:50756732-50757065	MCF-7	breast:	n/a	chr2:50756940-50756958 chr2:50756945-50756953 chr2:50756942-50756963
28	RAD21	chr2:50756706-50757140	Hela-S3	cervix:	n/a	chr2:50756941-50756960
29	RAD21	chr2:50756686-50757199	ECC-1	luminal epithelium:	n/a	chr2:50756941-50756960
30	CTCF	chr2:50756789-50757148	HCT-116	colon:	n/a	chr2:50756940-50756958 chr2:50756945-50756953 chr2:50756942-50756963
31	CTCF	chr2:50756792-50757020	MCF-7	breast:	n/a	chr2:50756940-50756958 chr2:50756945-50756953 chr2:50756942-50756963
32	RAD21	chr2:50756678-50757101	SK-N-SH_RA	brain:	n/a	chr2:50756941-50756960
33	SMC3	chr2:50756739-50757143	Hela-S3	cervix:	n/a	n/a
34	ZNF143	chr2:50756761-50757123	GM12878	blood:	n/a	n/a
35	CTCF	chr2:50756800-50756950	RPTEC	kidney:	n/a	n/a
36	CTCF	chr2:50756537-50757316	A549	lung:	n/a	chr2:50756940-50756958 chr2:50756945-50756953 chr2:50756942-50756963
37	RAD21	chr2:50756739-50757119	H1-hESC	embryonic stem cell:	n/a	chr2:50756941-50756960
38	CTCF	chr2:50756639-50757131	K562	blood:	n/a	chr2:50756940-50756958 chr2:50756945-50756953 chr2:50756942-50756963
39	CTCF	chr2:50756800-50756950	HFF-Myc	foreskin:	n/a	n/a
40	CTCF	chr2:50756780-50756930	GM12869	blood:	n/a	n/a
41	CTCF	chr2:50756786-50757025	Gliobla	brain:	n/a	chr2:50756940-50756958 chr2:50756945-50756953 chr2:50756942-50756963
42	CTCF	chr2:50756766-50757072	SK-N-SH_RA	brain:	n/a	chr2:50756940-50756958 chr2:50756945-50756953 chr2:50756942-50756963
43	CTCF	chr2:50756798-50757078	Medullo	brain:	n/a	chr2:50756940-50756958 chr2:50756945-50756953 chr2:50756942-50756963
44	CTCF	chr2:50756800-50756950	MCF-7	breast:	n/a	n/a
45	CTCF	chr2:50756780-50756930	NHLF	lung:	n/a	n/a
46	SIN3A	chr2:50756774-50756974	H1-hESC	embryonic stem cell:	n/a	n/a
47	CTCF	chr2:50756800-50756950	A549	lung:	n/a	n/a
48	RAD21	chr2:50756793-50757120	SK-N-SH_RA	brain:	n/a	chr2:50756941-50756960
49	E2F4	chr2:50756793-50757020	MCF10A-Er-Src	breast:	n/a	n/a
50	RAD21	chr2:50756733-50757222	IMR90	lung:	n/a	chr2:50756941-50756960

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:50756714..50757394-chr2:52022672..52023233,2	MCF-7	breast:

Variant related genes	Relation type
NRXN1	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1006138	0.85[ASN][1000 genomes]
rs1014430	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10168080	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10176959	0.83[ASN][1000 genomes]
rs10183541	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10187846	0.82[ASN][1000 genomes]
rs10190305	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10191072	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1019318	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10199840	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10207057	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10210592	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10211193	0.90[ASN][1000 genomes]
rs1030050	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12713104	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13012186	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13034257	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1984957	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2041869	0.82[ASN][1000 genomes]
rs2058751	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2058752	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2066948	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2111065	0.81[ASN][1000 genomes]
rs2111066	0.81[ASN][1000 genomes]
rs2160448	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2160449	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2216171	0.81[ASN][1000 genomes]
rs6545172	0.81[ASN][1000 genomes]
rs6545173	0.83[ASN][1000 genomes]
rs6545174	0.84[ASN][1000 genomes]
rs6545175	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6545176	0.88[ASN][1000 genomes]
rs6545177	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6545178	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6713061	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6722389	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6732076	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6753552	0.86[ASN][1000 genomes]
rs7564428	0.86[ASN][1000 genomes]
rs7566514	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7595040	0.81[ASN][1000 genomes]
rs759505	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs759506	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492164	chr2:50399251-51029090	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1000653	chr2:50417660-51083470	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv535693	chr2:50417660-51083470	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv948361	chr2:50611076-50785178	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv933786	chr2:50628354-50780185	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1010510	chr2:50649641-51011565	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv535694	chr2:50649641-51011565	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv532650	chr2:50675808-51136752	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv491644	chr2:50680795-50892906	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv498102	chr2:50680795-50937503	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv532651	chr2:50712339-50758351	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv532681	chr2:50715261-51172182	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv933959	chr2:50722885-50858529	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv915896	chr2:50725664-51057797	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv498101	chr2:50725729-50937503	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv933706	chr2:50755312-50765504	Active TSS Enhancers Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:50754000-50763200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr2:50754000-50763400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr2:50756000-50759800	Weak transcription	Fetal Brain Female	brain
4	chr2:50756200-50756800	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr2:50756400-50756800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr2:50756400-50756800	Enhancers	Pancreatic Islets	Pancreatic Islet
7	chr2:50756400-50757000	Enhancers	Brain Anterior Caudate	brain
8	chr2:50756600-50757000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:50756600-50757000	Enhancers	Brain Germinal Matrix	brain
10	chr2:50756600-50757000	Enhancers	Hela-S3	cervix
11	chr2:50756800-50757000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:50756800-50759600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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