Variant report

Variant	rs617604
Chromosome Location	chr6:4088349-4088350
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C6orf146-5	chr6:4088238-4088519	NONHSAT107299

Extended variants
information (count: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs101418	0.99[ASN][1000 genomes]
rs11755877	0.99[ASN][1000 genomes]
rs1204951	0.98[ASN][1000 genomes]
rs2326408	0.90[ASN][1000 genomes]
rs2473597	0.93[ASN][1000 genomes]
rs2745453	0.93[ASN][1000 genomes]
rs2745455	0.98[ASN][1000 genomes]
rs2783063	0.99[ASN][1000 genomes]
rs2783073	0.90[ASN][1000 genomes]
rs28878015	0.82[ASN][1000 genomes]
rs4959271	0.81[ASN][1000 genomes]
rs582008	0.82[ASN][1000 genomes]
rs583782	0.82[ASN][1000 genomes]
rs583881	0.82[ASN][1000 genomes]
rs584585	0.90[ASN][1000 genomes]
rs588158	0.86[ASN][1000 genomes]
rs589494	0.86[ASN][1000 genomes]
rs590675	0.93[ASN][1000 genomes]
rs592953	0.93[ASN][1000 genomes]
rs593291	0.91[ASN][1000 genomes]
rs594662	0.93[ASN][1000 genomes]
rs595413	0.93[ASN][1000 genomes]
rs608195	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs609946	0.93[ASN][1000 genomes]
rs611500	0.90[ASN][1000 genomes]
rs612022	0.90[ASN][1000 genomes]
rs612477	0.96[ASN][1000 genomes]
rs613028	0.91[ASN][1000 genomes]
rs613260	0.90[ASN][1000 genomes]
rs613709	0.90[ASN][1000 genomes]
rs617790	0.90[ASN][1000 genomes]
rs619439	0.90[ASN][1000 genomes]
rs619483	0.99[ASN][1000 genomes]
rs619873	0.90[ASN][1000 genomes]
rs620484	0.90[ASN][1000 genomes]
rs620901	0.91[ASN][1000 genomes]
rs621205	0.82[ASN][1000 genomes]
rs626080	0.91[ASN][1000 genomes]
rs627259	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs629362	0.90[ASN][1000 genomes]
rs633290	0.90[ASN][1000 genomes]
rs634114	0.80[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs634698	0.90[ASN][1000 genomes]
rs634970	0.82[ASN][1000 genomes]
rs638329	0.82[ASN][1000 genomes]
rs639905	0.93[ASN][1000 genomes]
rs643232	0.90[ASN][1000 genomes]
rs646385	0.82[ASN][1000 genomes]
rs648900	0.90[ASN][1000 genomes]
rs649725	0.90[ASN][1000 genomes]
rs651246	0.93[ASN][1000 genomes]
rs653431	0.93[ASN][1000 genomes]
rs654621	0.93[ASN][1000 genomes]
rs654982	0.93[ASN][1000 genomes]
rs659025	0.90[ASN][1000 genomes]
rs659051	0.82[ASN][1000 genomes]
rs659305	0.90[ASN][1000 genomes]
rs660560	0.90[ASN][1000 genomes]
rs660957	0.82[ASN][1000 genomes]
rs661404	0.90[ASN][1000 genomes]
rs661657	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs662834	0.99[ASN][1000 genomes]
rs664299	0.88[ASN][1000 genomes]
rs664635	0.82[ASN][1000 genomes]
rs664839	0.91[ASN][1000 genomes]
rs664898	0.82[ASN][1000 genomes]
rs665728	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs665894	0.98[ASN][1000 genomes]
rs666254	0.95[ASN][1000 genomes]
rs668070	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs670932	0.93[ASN][1000 genomes]
rs671364	0.93[ASN][1000 genomes]
rs674543	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs676683	0.90[ASN][1000 genomes]
rs678285	0.82[ASN][1000 genomes]
rs679303	0.82[ASN][1000 genomes]
rs688176	0.91[ASN][1000 genomes]
rs689308	0.90[ASN][1000 genomes]
rs694058	0.82[ASN][1000 genomes]
rs694903	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs707991	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7166	0.90[ASN][1000 genomes]
rs7744628	0.90[ASN][1000 genomes]
rs7756630	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7757606	0.90[ASN][1000 genomes]
rs853416	0.90[ASN][1000 genomes]
rs853417	0.90[ASN][1000 genomes]
rs853418	0.82[ASN][1000 genomes]
rs9328220	0.90[ASN][1000 genomes]
rs9378395	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9405219	0.99[ASN][1000 genomes]
rs9405701	0.82[ASN][1000 genomes]
rs942475	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532020	chr6:3417520-4140257	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv462615	chr6:4052383-4096678	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv600860	chr6:4052383-4096678	Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1030104	chr6:4062894-4240269	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4079400-4092000	Weak transcription	Right Atrium	heart
2	chr6:4085000-4088800	Weak transcription	Fetal Intestine Large	intestine
3	chr6:4085200-4088400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr6:4085200-4088800	Weak transcription	Duodenum Mucosa	Duodenum
5	chr6:4086400-4090200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:4086800-4089800	Enhancers	Stomach Mucosa	stomach
7	chr6:4087600-4088600	Enhancers	Gastric	stomach
8	chr6:4087800-4088800	Weak transcription	Pancreas	Pancrea
9	chr6:4088200-4088800	Enhancers	Sigmoid Colon	Sigmoid Colon
10	chr6:4088200-4088800	Enhancers	Small Intestine	intestine

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