Variant report

Variant	rs11902709
Chromosome Location	chr2:179608207-179608208
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:179602765..179606051-chr2:179607318..179610882,3	K562	blood:
2	chr2:179603997..179606051-chr2:179606737..179608818,2	K562	blood:
3	chr2:179602021..179604005-chr2:179606388..179608264,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC141-2	chr2:179607321-179609139	NONHSAT075816

Variant related genes	Relation type
ENSG00000237298	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10171049	0.87[CHB][hapmap];0.83[CHD][hapmap];0.87[ASN][1000 genomes]
rs10803917	0.90[LWK][hapmap]
rs11902672	1.00[ASW][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs12464703	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12470905	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12476289	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16866479	0.88[YRI][hapmap];0.92[AFR][1000 genomes]
rs16866485	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs16866497	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.93[MEX][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16866532	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16866534	0.90[LWK][hapmap]
rs1883084	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2243804	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2253324	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2255480	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2291304	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2291305	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2291308	1.00[CEU][hapmap];0.89[CHD][hapmap];0.93[MEX][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2291310	0.80[CHB][hapmap];0.81[ASN][1000 genomes]
rs2306636	1.00[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2562829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2562832	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2562833	0.93[ASN][1000 genomes]
rs2562835	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2562837	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2562841	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2562842	0.97[ASN][1000 genomes]
rs2562852	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2562853	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2562854	0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2627034	0.97[ASN][1000 genomes]
rs2627037	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2627040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2627041	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2627042	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2627044	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2742328	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2742329	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2742330	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2742332	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2742333	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2742334	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2742335	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2742336	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2742337	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2742339	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2742340	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2742341	0.98[ASN][1000 genomes]
rs2742342	0.98[ASN][1000 genomes]
rs2742343	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2742344	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2742345	1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2742347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2742357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3754953	0.87[CHB][hapmap];0.81[CHD][hapmap];0.87[ASN][1000 genomes]
rs3769860	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4894036	0.82[AFR][1000 genomes]
rs4894037	0.87[CHB][hapmap];0.87[ASN][1000 genomes]
rs4894043	0.90[LWK][hapmap]
rs55863869	0.92[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs55895721	0.92[AFR][1000 genomes]
rs56030306	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56120016	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56142888	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66677602	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72647839	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72647889	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72648906	0.85[AFR][1000 genomes]
rs72648917	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72648932	0.92[AFR][1000 genomes]
rs7585334	0.87[CHB][hapmap];0.81[CHD][hapmap];0.87[ASN][1000 genomes]
rs7604033	0.80[CHB][hapmap]
rs922984	0.87[CHB][hapmap];0.87[ASN][1000 genomes]
rs922986	0.85[LWK][hapmap]

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	esv2757841	chr2:179409072-179608242	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2759103	chr2:179409072-179608242	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv834470	chr2:179555152-179728726	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv934108	chr2:179556852-179729925	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179483200-179655400	Weak transcription	Adipose Nuclei	Adipose
2	chr2:179493000-179620800	Weak transcription	HSMM	muscle
3	chr2:179533600-179669200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr2:179577800-179640800	Weak transcription	Fetal Intestine Large	intestine
5	chr2:179584200-179616200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr2:179585200-179615800	Weak transcription	Primary B cells from peripheral blood	blood
7	chr2:179588200-179622800	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr2:179590800-179640400	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr2:179591800-179608400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
10	chr2:179598000-179614200	Weak transcription	Primary B cells from cord blood	blood
11	chr2:179598600-179622200	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr2:179600800-179616400	Weak transcription	Psoas Muscle	Psoas
13	chr2:179600800-179621200	Weak transcription	Pancreas	Pancrea
14	chr2:179603000-179610400	Weak transcription	Aorta	Aorta
15	chr2:179603200-179614800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr2:179603400-179612400	Weak transcription	Primary T cells from cord blood	blood
17	chr2:179605400-179662400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:179606000-179610200	Weak transcription	Fetal Muscle Leg	muscle
19	chr2:179606200-179614600	Weak transcription	Right Ventricle	heart
20	chr2:179606400-179610200	Weak transcription	Fetal Heart	heart
21	chr2:179606400-179610400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr2:179606600-179609800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr2:179606600-179610200	Weak transcription	Left Ventricle	heart
24	chr2:179606600-179610400	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links