Variant report

Variant	rs7754298
Chromosome Location	chr6:4289773-4289774
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:4279688..4281240-chr6:4289291..4291917,2	MCF-7	breast:
2	chr6:4283994..4286651-chr6:4287525..4290024,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ECI2-8	chr6:4286984-4290099	l_3095_chr6:4286983-4292375_heart
2	lnc-C6orf201-16	chr6:4288783-4292377	NONHSAT107382

Extended variants
information (count: 120 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10080414	0.93[EUR][1000 genomes]
rs10223886	0.93[EUR][1000 genomes]
rs10428864	0.84[EUR][1000 genomes]
rs1072903	0.93[EUR][1000 genomes]
rs11961149	0.96[EUR][1000 genomes]
rs11970375	0.96[EUR][1000 genomes]
rs11970430	0.96[EUR][1000 genomes]
rs1591412	0.87[EUR][1000 genomes]
rs17500205	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17565229	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1832060	0.87[EUR][1000 genomes]
rs2210761	0.95[EUR][1000 genomes]
rs2210762	0.95[EUR][1000 genomes]
rs2326473	0.87[EUR][1000 genomes]
rs4255019	0.95[EUR][1000 genomes]
rs4256473	0.95[EUR][1000 genomes]
rs4443539	0.95[EUR][1000 genomes]
rs4475361	0.95[EUR][1000 genomes]
rs4526241	0.87[EUR][1000 genomes]
rs4596533	0.95[EUR][1000 genomes]
rs4629733	0.95[EUR][1000 genomes]
rs4959937	0.93[EUR][1000 genomes]
rs4959938	0.93[EUR][1000 genomes]
rs57509474	0.95[EUR][1000 genomes]
rs58402712	0.95[EUR][1000 genomes]
rs59033141	0.81[AFR][1000 genomes]
rs59706955	0.95[EUR][1000 genomes]
rs60023788	0.95[EUR][1000 genomes]
rs61604146	0.95[EUR][1000 genomes]
rs6597046	0.96[EUR][1000 genomes]
rs6597047	0.96[EUR][1000 genomes]
rs6597048	0.96[EUR][1000 genomes]
rs6913742	0.93[EUR][1000 genomes]
rs6916181	0.95[EUR][1000 genomes]
rs6922330	0.86[EUR][1000 genomes]
rs6931784	0.95[EUR][1000 genomes]
rs6934489	0.94[EUR][1000 genomes]
rs6934652	0.94[EUR][1000 genomes]
rs73358820	0.95[EUR][1000 genomes]
rs73358823	0.95[EUR][1000 genomes]
rs73358854	0.95[EUR][1000 genomes]
rs73360930	0.96[EUR][1000 genomes]
rs73360933	0.96[EUR][1000 genomes]
rs73360945	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7759565	0.93[EUR][1000 genomes]
rs7763657	0.92[EUR][1000 genomes]
rs7763789	0.95[EUR][1000 genomes]
rs7765457	0.95[EUR][1000 genomes]
rs913405	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9328227	0.95[EUR][1000 genomes]
rs9328229	0.95[EUR][1000 genomes]
rs9328230	0.98[EUR][1000 genomes]
rs9328231	0.96[EUR][1000 genomes]
rs9328232	0.96[EUR][1000 genomes]
rs9328233	0.96[EUR][1000 genomes]
rs9328236	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9392032	0.94[EUR][1000 genomes]
rs9392578	0.88[EUR][1000 genomes]
rs9392580	0.93[EUR][1000 genomes]
rs9405228	0.94[EUR][1000 genomes]
rs9502148	0.95[EUR][1000 genomes]
rs9502149	0.95[EUR][1000 genomes]
rs9502150	0.95[EUR][1000 genomes]
rs9502151	0.95[EUR][1000 genomes]
rs9502152	0.95[EUR][1000 genomes]
rs9502153	0.94[EUR][1000 genomes]
rs9502154	0.94[EUR][1000 genomes]
rs9502157	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9502158	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9502159	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9502160	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9502161	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9502163	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9503982	0.87[EUR][1000 genomes]
rs9503983	0.87[EUR][1000 genomes]
rs9503984	0.87[EUR][1000 genomes]
rs9503985	0.84[EUR][1000 genomes]
rs9503993	0.94[EUR][1000 genomes]
rs9503994	0.94[EUR][1000 genomes]
rs9503995	0.94[EUR][1000 genomes]
rs9503996	0.95[EUR][1000 genomes]
rs9504005	0.96[EUR][1000 genomes]
rs9504006	0.96[EUR][1000 genomes]
rs9504007	0.95[EUR][1000 genomes]
rs9504008	0.95[EUR][1000 genomes]
rs9504009	0.95[EUR][1000 genomes]
rs9504010	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9504022	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9504025	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9504033	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422457	chr6:4100333-4377396	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv600861	chr6:4238488-4469641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv462618	chr6:4238488-4472587	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv600862	chr6:4238488-4472587	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv949364	chr6:4253413-4466981	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv600863	chr6:4255387-4472587	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv1027498	chr6:4255640-4471635	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	esv2763995	chr6:4255640-4474114	Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv1020205	chr6:4255640-4474114	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv600864	chr6:4255708-4464630	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv516402	chr6:4255708-4472587	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv462619	chr6:4255708-4472587	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv600865	chr6:4255708-4472587	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	nsv462620	chr6:4255708-4481421	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
15	nsv600866	chr6:4255708-4481421	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
16	nsv600867	chr6:4255725-4464630	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
17	nsv462621	chr6:4255725-4472587	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
18	nsv600868	chr6:4255725-4472587	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
19	nsv1029501	chr6:4255745-4471635	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
20	nsv432845	chr6:4255905-4471472	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
21	nsv1030655	chr6:4257190-4473701	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
22	nsv538108	chr6:4257190-4473701	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
23	nsv1030840	chr6:4257390-4473562	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
24	nsv538109	chr6:4257390-4473562	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
25	nsv1026890	chr6:4259075-4471635	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
26	nsv1030588	chr6:4264933-4455210	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
27	nsv1021257	chr6:4264933-4473384	Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
28	nsv538110	chr6:4264933-4473384	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
29	nsv916553	chr6:4269714-4437920	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
30	nsv1016621	chr6:4277411-4473384	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7754298	PECI	cis	cerebellum	SCAN
rs7754298	CDYL	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4284800-4291600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:4288400-4291400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr6:4288400-4291600	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr6:4288400-4291600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:4288400-4291600	Weak transcription	Placenta	Placenta
6	chr6:4288400-4291600	Weak transcription	K562	blood
7	chr6:4288400-4291800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:4288400-4292600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr6:4288600-4291400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr6:4288600-4291600	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr6:4288600-4294400	Weak transcription	Fetal Muscle Trunk	muscle
12	chr6:4288600-4295600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr6:4288800-4291600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr6:4288800-4295200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr6:4289000-4291400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr6:4289000-4291600	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr6:4289000-4291600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:4289000-4294600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr6:4289200-4291800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links