Variant report

Variant	rs2852505
Chromosome Location	chr6:101843474-101843475
allele	C/G
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	RAD21	chr6:101843280-101843505	SK-N-SH_RA	brain:	n/a	chr6:101843412-101843425 chr6:101843414-101843424 chr6:101843409-101843428
2	POLR2A	chr6:101843409-101843672	MCF10A-Er-Src	breast:	n/a	n/a
3	CTCF	chr6:101843360-101843510	NHDF-neo	bronchial:	n/a	chr6:101843411-101843419 chr6:101843411-101843424 chr6:101843408-101843426
4	CTCF	chr6:101843258-101843577	GM12878	blood:	n/a	chr6:101843411-101843419 chr6:101843411-101843424 chr6:101843408-101843426
5	CTCF	chr6:101843440-101843590	HMEC	breast:	n/a	n/a
6	CTCF	chr6:101843400-101843550	HEK293	kidney:	n/a	chr6:101843411-101843419 chr6:101843411-101843424 chr6:101843408-101843426
7	MXI1	chr6:101840627-101843576	SK-N-SH	brain:	n/a	n/a
8	CTCF	chr6:101843360-101843510	HMF	breast:	n/a	chr6:101843411-101843419 chr6:101843411-101843424 chr6:101843408-101843426
9	CTCF	chr6:101843380-101843530	AG10803	skin:	n/a	chr6:101843411-101843419 chr6:101843411-101843424 chr6:101843408-101843426
10	CTCF	chr6:101843340-101843490	NHEK	skin:	n/a	chr6:101843411-101843419 chr6:101843411-101843424 chr6:101843408-101843426
11	RAD21	chr6:101843251-101843592	Hela-S3	cervix:	n/a	chr6:101843412-101843425 chr6:101843414-101843424 chr6:101843409-101843428
12	E2F4	chr6:101843341-101843582	MCF10A-Er-Src	breast:	n/a	n/a
13	CTCF	chr6:101843340-101843490	AG09309	skin:	n/a	chr6:101843411-101843419 chr6:101843411-101843424 chr6:101843408-101843426
14	CTCF	chr6:101843310-101843495	Hela-S3	cervix:	n/a	chr6:101843411-101843419 chr6:101843411-101843424 chr6:101843408-101843426
15	CTCF	chr6:101843344-101843486	HUVEC	blood vessel:	n/a	chr6:101843411-101843419 chr6:101843411-101843424 chr6:101843408-101843426
16	CTCF	chr6:101843400-101843550	HCPEpiC	choroid plexus:	n/a	chr6:101843411-101843419 chr6:101843411-101843424 chr6:101843408-101843426
17	CTCF	chr6:101843244-101843656	MCF-7	breast:	n/a	chr6:101843411-101843419 chr6:101843411-101843424 chr6:101843408-101843426
18	CTCF	chr6:101843340-101843490	HMEC	breast:	n/a	chr6:101843411-101843419 chr6:101843411-101843424 chr6:101843408-101843426
19	CTCF	chr6:101843340-101843490	HPAF	blood vessel:	n/a	chr6:101843411-101843419 chr6:101843411-101843424 chr6:101843408-101843426
20	RAD21	chr6:101843283-101843509	A549	lung:	n/a	chr6:101843412-101843425 chr6:101843414-101843424 chr6:101843409-101843428
21	CTCF	chr6:101843360-101843510	AG04450	lung:	n/a	chr6:101843411-101843419 chr6:101843411-101843424 chr6:101843408-101843426
22	CTCF	chr6:101843360-101843510	SAEC	small airway:	n/a	chr6:101843411-101843419 chr6:101843411-101843424 chr6:101843408-101843426
23	CTCF	chr6:101843360-101843510	GM06990	blood:	n/a	chr6:101843411-101843419 chr6:101843411-101843424 chr6:101843408-101843426
24	CTCF	chr6:101843326-101843489	LNCaP	prostate:	n/a	chr6:101843411-101843419 chr6:101843411-101843424 chr6:101843408-101843426
25	CTCF	chr6:101843380-101843530	HCFaa	heart:	n/a	chr6:101843411-101843419 chr6:101843411-101843424 chr6:101843408-101843426
26	CTCF	chr6:101843234-101843643	IMR90	lung:	n/a	chr6:101843411-101843419 chr6:101843411-101843424 chr6:101843408-101843426
27	CTCF	chr6:101843360-101843510	BE2_C	brain:	n/a	chr6:101843411-101843419 chr6:101843411-101843424 chr6:101843408-101843426
28	SMC3	chr6:101842757-101843792	SK-N-SH	brain:	n/a	chr6:101843410-101843424
29	CTCF	chr6:101843360-101843510	HBMEC	blood vessel:	n/a	chr6:101843411-101843419 chr6:101843411-101843424 chr6:101843408-101843426
30	CTCF	chr6:101843341-101843531	Medullo	brain:	n/a	chr6:101843411-101843419 chr6:101843411-101843424 chr6:101843408-101843426
31	RAD21	chr6:101842901-101844001	SK-N-SH	brain:	n/a	chr6:101843412-101843425 chr6:101843414-101843424 chr6:101843409-101843428
32	CTCF	chr6:101843340-101843490	HMF	breast:	n/a	chr6:101843411-101843419 chr6:101843411-101843424 chr6:101843408-101843426
33	CTCF	chr6:101843360-101843510	HRPEpiC	eye:	n/a	chr6:101843411-101843419 chr6:101843411-101843424 chr6:101843408-101843426
34	CTCF	chr6:101843360-101843510	Hela-S3	cervix:	n/a	chr6:101843411-101843419 chr6:101843411-101843424 chr6:101843408-101843426
35	SMC3	chr6:101843279-101843579	Hela-S3	cervix:	n/a	chr6:101843410-101843424
36	CTCF	chr6:101843360-101843510	SK-N-SH_RA	brain:	n/a	chr6:101843411-101843419 chr6:101843411-101843424 chr6:101843408-101843426
37	CTCF	chr6:101843420-101843570	RPTEC	kidney:	n/a	n/a
38	CTCF	chr6:101843334-101843485	LNCaP	prostate:	n/a	chr6:101843411-101843419 chr6:101843411-101843424 chr6:101843408-101843426
39	CTCF	chr6:101843400-101843550	HRPEpiC	eye:	n/a	chr6:101843411-101843419 chr6:101843411-101843424 chr6:101843408-101843426

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:101839704..101841744-chr6:101842658..101845506,3	K562	blood:

Variant related genes	Relation type
GRIK2	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10457930	1.00[ASN][1000 genomes]
rs12204255	1.00[ASN][1000 genomes]
rs12208565	1.00[ASN][1000 genomes]
rs1948050	0.82[EUR][1000 genomes]
rs2254178	1.00[ASN][1000 genomes]
rs2518173	0.82[EUR][1000 genomes]
rs2518319	0.82[EUR][1000 genomes]
rs2579929	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2629982	0.82[EUR][1000 genomes]
rs2764271	1.00[ASN][1000 genomes]
rs2787573	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852497	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852500	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2852502	0.95[EUR][1000 genomes]
rs2852503	0.95[EUR][1000 genomes]
rs2852504	0.97[EUR][1000 genomes]
rs2852506	0.97[EUR][1000 genomes]
rs2852507	0.97[EUR][1000 genomes]
rs2852509	0.97[EUR][1000 genomes]
rs2852510	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852511	0.97[EUR][1000 genomes]
rs2852512	0.97[EUR][1000 genomes]
rs2852513	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2852514	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs496596	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs503387	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs566507	0.81[EUR][1000 genomes]
rs570556	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs579069	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62419629	1.00[ASN][1000 genomes]
rs626262	1.00[ASN][1000 genomes]
rs632956	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs643101	1.00[ASN][1000 genomes]
rs658318	1.00[ASN][1000 genomes]
rs661064	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs662360	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs675259	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs687497	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs697438	1.00[ASN][1000 genomes]
rs72958632	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020400	chr6:101172705-101981665	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv538390	chr6:101172705-101981665	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:101840000-101843600	Active TSS	Right Atrium	heart
2	chr6:101842000-101843800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:101842000-101845000	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr6:101842200-101843800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr6:101842200-101846600	Weak transcription	Pancreas	Pancrea
6	chr6:101842200-101849600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr6:101842400-101844200	Bivalent/Poised TSS	Fetal Brain Male	brain
8	chr6:101842400-101849600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:101842800-101843600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr6:101842800-101845400	Active TSS	Fetal Brain Female	brain
11	chr6:101842800-101846800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr6:101843200-101846000	Weak transcription	Brain Angular Gyrus	brain
13	chr6:101843200-101846400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:101843200-101846600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:101843200-101846800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr6:101843400-101843800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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