Variant report

Variant	rs2065219
Chromosome Location	chr6:4405619-4405620
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	chr6:4398942..4400523-chr6:4402964..4405624,2	K562	blood:
2	chr6:4401864..4404753-chr6:4405538..4407059,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C6orf201-21	chr6:4405580-4406503	NONHSAT107419

Extended variants
information (count: 100 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs11242924	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs11242925	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11242927	0.87[ASN][1000 genomes]
rs11242928	0.92[ASN][1000 genomes]
rs11242929	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11242930	0.92[ASN][1000 genomes]
rs11242938	0.91[EUR][1000 genomes]
rs12190411	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12195432	0.91[ASN][1000 genomes]
rs12207441	0.91[EUR][1000 genomes]
rs12524545	0.92[ASN][1000 genomes]
rs1265194	0.86[EUR][1000 genomes]
rs13214482	0.91[EUR][1000 genomes]
rs1330786	0.91[GIH][hapmap]
rs1330792	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1411654	0.90[EUR][1000 genomes]
rs1581971	0.80[EUR][1000 genomes]
rs170949	0.84[EUR][1000 genomes]
rs17567855	0.84[ASN][1000 genomes]
rs2065218	0.92[ASN][1000 genomes]
rs2150233	0.80[EUR][1000 genomes]
rs383470	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs415338	0.84[EUR][1000 genomes]
rs4286821	0.91[EUR][1000 genomes]
rs446293	0.85[EUR][1000 genomes]
rs492603	0.84[ASN][1000 genomes]
rs4959284	0.92[ASN][1000 genomes]
rs4959286	0.92[ASN][1000 genomes]
rs4959950	0.84[ASN][1000 genomes]
rs4959952	0.92[ASN][1000 genomes]
rs4959953	0.97[ASN][1000 genomes]
rs4959961	0.81[EUR][1000 genomes]
rs4959962	0.86[EUR][1000 genomes]
rs501141	0.84[ASN][1000 genomes]
rs516527	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs550170	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs552839	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs553764	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs553844	0.84[ASN][1000 genomes]
rs55830017	0.92[ASN][1000 genomes]
rs56314957	0.92[ASN][1000 genomes]
rs58613216	0.84[ASN][1000 genomes]
rs59425532	0.86[EUR][1000 genomes]
rs61711492	0.90[ASN][1000 genomes]
rs6597055	0.90[EUR][1000 genomes]
rs66773553	0.92[ASN][1000 genomes]
rs6913210	0.81[EUR][1000 genomes]
rs6914316	0.81[EUR][1000 genomes]
rs6921285	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6924842	0.89[EUR][1000 genomes]
rs6937848	0.81[EUR][1000 genomes]
rs7450619	0.91[EUR][1000 genomes]
rs7453615	0.91[EUR][1000 genomes]
rs7754765	0.87[EUR][1000 genomes]
rs885183	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs885184	0.85[ASN][1000 genomes]
rs914047	0.85[ASN][1000 genomes]
rs9378867	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9378874	0.81[EUR][1000 genomes]
rs9378875	0.80[EUR][1000 genomes]
rs9392596	0.90[EUR][1000 genomes]
rs9405235	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9405731	0.81[EUR][1000 genomes]
rs9504074	0.89[EUR][1000 genomes]
rs9504077	0.91[ASN][1000 genomes]
rs9504093	0.91[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:34 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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
26	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
27	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
28	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
29	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
30	nsv600869	chr6:4294450-4430623	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
31	nsv883413	chr6:4371622-4474114	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
32	nsv1021743	chr6:4382308-4494308	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
33	nsv538111	chr6:4382308-4494308	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
34	nsv600870	chr6:4391872-4429310	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2065219	LY86	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4395600-4405800	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr6:4397200-4406800	Enhancers	Fetal Muscle Leg	muscle
3	chr6:4402400-4406600	Enhancers	Brain Anterior Caudate	brain
4	chr6:4402800-4406600	Enhancers	Brain Hippocampus Middle	brain
5	chr6:4403200-4405800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr6:4403200-4405800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:4403200-4405800	Weak transcription	Fetal Lung	lung
8	chr6:4403200-4405800	Weak transcription	Lung	lung
9	chr6:4403200-4406000	Weak transcription	Pancreas	Pancrea
10	chr6:4403200-4406000	Weak transcription	Spleen	Spleen
11	chr6:4403200-4413800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:4403600-4406600	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr6:4403800-4418600	Weak transcription	NHLF	lung
14	chr6:4404400-4406200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:4404400-4407000	Weak transcription	Adipose Nuclei	Adipose
16	chr6:4404800-4405800	Weak transcription	Brain Substantia Nigra	brain
17	chr6:4404800-4405800	Weak transcription	Fetal Stomach	stomach
18	chr6:4404800-4406000	Weak transcription	Right Atrium	heart
19	chr6:4405200-4406800	Enhancers	Fetal Muscle Trunk	muscle
20	chr6:4405400-4406400	Enhancers	Brain Cingulate Gyrus	brain
21	chr6:4405400-4406600	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr6:4405400-4406600	Enhancers	HSMMtube	muscle
23	chr6:4405600-4405800	Enhancers	Primary B cells from peripheral blood	blood
24	chr6:4405600-4406000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr6:4405600-4406000	Enhancers	Psoas Muscle	Psoas
26	chr6:4405600-4406200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr6:4405600-4406200	Enhancers	Colonic Mucosa	Colon
28	chr6:4405600-4406200	Enhancers	Right Ventricle	heart
29	chr6:4405600-4406400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr6:4405600-4406400	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr6:4405600-4406400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr6:4405600-4406600	Enhancers	H1 Cell Line	embryonic stem cell
33	chr6:4405600-4406600	Enhancers	Brain Angular Gyrus	brain
34	chr6:4405600-4406600	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr6:4405600-4406600	Enhancers	HSMM	muscle
36	chr6:4405600-4406800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links