Variant report

Variant	rs2246642
Chromosome Location	chr6:29949518-29949519
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:29944005..29947343-chr6:29947938..29951140,5	K562	blood:
2	chr6:29941687..29943484-chr6:29948352..29949943,2	K562	blood:
3	chr6:29943871..29947343-chr6:29947953..29952410,7	K562	blood:
4	chr6:29937399..29939324-chr6:29949163..29951713,2	K562	blood:

Variant related genes	Relation type
ENSG00000204625	Chromatin interaction

Extended variants
information (count: 197 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:174)

rs_ID	r²[population]
rs10807060	0.84[ASN][1000 genomes]
rs10947040	0.89[ASN][1000 genomes]
rs10947042	0.85[ASN][1000 genomes]
rs10947043	0.86[ASN][1000 genomes]
rs10947045	0.84[ASN][1000 genomes]
rs10947046	0.84[ASN][1000 genomes]
rs10947047	0.84[ASN][1000 genomes]
rs11751331	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11753431	0.84[ASN][1000 genomes]
rs11753957	0.84[ASN][1000 genomes]
rs11753960	0.84[ASN][1000 genomes]
rs11754605	0.84[ASN][1000 genomes]
rs11754620	0.82[ASN][1000 genomes]
rs11755337	0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11755374	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11755549	0.84[ASN][1000 genomes]
rs11755961	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11755966	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11755984	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11755992	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11756025	0.93[ASN][1000 genomes]
rs11757750	0.93[ASN][1000 genomes]
rs11757792	0.80[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11758493	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11759388	0.84[ASN][1000 genomes]
rs11759891	0.93[ASN][1000 genomes]
rs11760176	0.84[ASN][1000 genomes]
rs11962771	0.84[ASN][1000 genomes]
rs11964113	0.80[ASN][1000 genomes]
rs11965458	0.84[ASN][1000 genomes]
rs11965524	0.84[ASN][1000 genomes]
rs11965585	0.84[ASN][1000 genomes]
rs11965659	0.84[ASN][1000 genomes]
rs11967317	0.84[ASN][1000 genomes]
rs11967331	0.84[ASN][1000 genomes]
rs12110437	0.89[ASN][1000 genomes]
rs12111210	0.85[ASN][1000 genomes]
rs12661053	0.84[ASN][1000 genomes]
rs12661394	0.90[ASN][1000 genomes]
rs12661402	0.90[ASN][1000 genomes]
rs12661411	0.94[ASN][1000 genomes]
rs12661609	0.84[ASN][1000 genomes]
rs12662336	0.94[ASN][1000 genomes]
rs12662947	0.94[ASN][1000 genomes]
rs12662967	0.94[ASN][1000 genomes]
rs12663252	0.84[ASN][1000 genomes]
rs12664166	0.91[ASN][1000 genomes]
rs12664794	0.84[ASN][1000 genomes]
rs12664967	0.83[ASN][1000 genomes]
rs12665171	0.80[ASN][1000 genomes]
rs12665186	0.90[ASN][1000 genomes]
rs12665444	0.86[ASN][1000 genomes]
rs165256	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17180241	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17180542	0.90[ASN][1000 genomes]
rs17180577	0.90[ASN][1000 genomes]
rs17180759	0.93[ASN][1000 genomes]
rs17180794	0.94[ASN][1000 genomes]
rs17180864	0.89[ASN][1000 genomes]
rs17186930	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs17186937	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs17186944	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs17186979	0.94[ASN][1000 genomes]
rs17187021	0.93[ASN][1000 genomes]
rs17187077	0.94[ASN][1000 genomes]
rs17187141	0.94[ASN][1000 genomes]
rs17187252	0.89[ASN][1000 genomes]
rs17187349	0.84[ASN][1000 genomes]
rs17187488	0.84[ASN][1000 genomes]
rs17187523	0.84[ASN][1000 genomes]
rs17193851	0.84[ASN][1000 genomes]
rs17193886	0.82[ASN][1000 genomes]
rs1974574	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2108691	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2245952	0.86[ASN][1000 genomes]
rs2246199	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2246638	0.83[AMR][1000 genomes]
rs2256902	0.82[AMR][1000 genomes]
rs2275851	0.80[ASN][1000 genomes]
rs2508034	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2517809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517810	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523961	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2524005	0.81[JPT][hapmap]
rs2571430	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2735069	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2735072	0.85[ASN][1000 genomes]
rs2735074	0.91[ASN][1000 genomes]
rs28698859	0.86[ASN][1000 genomes]
rs28749538	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34513540	0.86[ASN][1000 genomes]
rs34894339	0.94[ASN][1000 genomes]
rs35144883	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs35356382	0.90[ASN][1000 genomes]
rs35480831	0.90[ASN][1000 genomes]
rs35574636	0.86[ASN][1000 genomes]
rs35685401	0.91[ASN][1000 genomes]
rs35763150	0.84[ASN][1000 genomes]
rs35796574	0.89[ASN][1000 genomes]
rs3734830	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs3734831	0.93[ASN][1000 genomes]
rs3734833	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs3734834	0.94[ASN][1000 genomes]
rs3765608	0.84[ASN][1000 genomes]
rs379221	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs419862	0.95[ASN][1000 genomes]
rs423808	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs427290	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55760574	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs56015532	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs56052612	0.91[ASN][1000 genomes]
rs57035982	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs57080532	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs57680173	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs57927905	0.88[ASN][1000 genomes]
rs58161185	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs58314476	0.84[ASN][1000 genomes]
rs58555592	0.84[ASN][1000 genomes]
rs58858573	0.89[ASN][1000 genomes]
rs58867136	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs58980848	0.84[ASN][1000 genomes]
rs60265332	0.84[ASN][1000 genomes]
rs60477028	0.84[ASN][1000 genomes]
rs60587228	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs61704409	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6457138	0.84[ASN][1000 genomes]
rs6902901	0.84[ASN][1000 genomes]
rs6911583	0.89[ASN][1000 genomes]
rs6912001	0.84[ASN][1000 genomes]
rs6917877	0.84[ASN][1000 genomes]
rs6928966	0.84[ASN][1000 genomes]
rs6931672	0.84[ASN][1000 genomes]
rs6932091	0.84[ASN][1000 genomes]
rs6933897	0.84[ASN][1000 genomes]
rs6940552	0.84[ASN][1000 genomes]
rs6940956	0.85[ASN][1000 genomes]
rs72502507	0.86[ASN][1000 genomes]
rs72502509	0.86[ASN][1000 genomes]
rs73410503	0.91[ASN][1000 genomes]
rs73410515	0.89[ASN][1000 genomes]
rs73410518	0.93[ASN][1000 genomes]
rs73410524	0.91[ASN][1000 genomes]
rs73410525	0.94[ASN][1000 genomes]
rs73410528	0.94[ASN][1000 genomes]
rs73410530	0.90[ASN][1000 genomes]
rs73414461	0.84[ASN][1000 genomes]
rs73414465	0.84[ASN][1000 genomes]
rs73416498	0.84[ASN][1000 genomes]
rs73416501	0.84[ASN][1000 genomes]
rs73420421	0.84[ASN][1000 genomes]
rs73420434	0.84[ASN][1000 genomes]
rs73420439	0.84[ASN][1000 genomes]
rs73428121	0.94[ASN][1000 genomes]
rs73428122	0.94[ASN][1000 genomes]
rs73428125	0.94[ASN][1000 genomes]
rs73428151	0.89[ASN][1000 genomes]
rs73428152	0.94[ASN][1000 genomes]
rs73725904	0.94[ASN][1000 genomes]
rs73725908	0.91[ASN][1000 genomes]
rs73725910	0.93[ASN][1000 genomes]
rs73725912	0.91[ASN][1000 genomes]
rs73725917	0.94[ASN][1000 genomes]
rs73725921	0.90[ASN][1000 genomes]
rs73725930	0.80[ASN][1000 genomes]
rs73725953	0.84[ASN][1000 genomes]
rs73725970	0.84[ASN][1000 genomes]
rs73725984	0.84[ASN][1000 genomes]
rs7742712	0.84[ASN][1000 genomes]
rs7742799	0.84[ASN][1000 genomes]
rs7746555	0.83[ASN][1000 genomes]
rs7750582	0.83[ASN][1000 genomes]
rs7762851	0.84[ASN][1000 genomes]
rs7764237	0.84[ASN][1000 genomes]
rs9261134	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427749	chr6:29659525-29975144	Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	esv3332677	chr6:29733187-29961463	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3430372	chr6:29759523-29974277	Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	esv2758040	chr6:29792434-29975144	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	esv2759412	chr6:29792434-29975144	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	esv3391180	chr6:29798321-29977430	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	esv1845786	chr6:29817123-29955129	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	esv1848127	chr6:29817323-29966451	Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv508398	chr6:29825777-30003403	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	esv3369212	chr6:29827361-29960177	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
11	esv2757159	chr6:29834472-29965501	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
12	esv3376588	chr6:29834667-29964324	Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
13	nsv10810	chr6:29837465-29961415	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
14	nsv870444	chr6:29842885-29949545	Strong transcription Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
15	esv3373906	chr6:29884407-29977070	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
16	esv2641340	chr6:29913287-29978544	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
17	esv3378806	chr6:29913464-29978179	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
18	esv3496792	chr6:29913818-29977071	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
19	esv3496793	chr6:29913818-29977071	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
20	nsv1031115	chr6:29934199-30058223	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
21	nsv538172	chr6:29934199-30058223	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
22	esv1799283	chr6:29938777-29959935	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
23	esv3326087	chr6:29947573-29951271	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2246642	ZNRD1	cis	multi-tissue	Pritchard
rs2246642	ZNRD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29945400-29950200	Weak transcription	Right Atrium	heart
2	chr6:29945600-29966400	Weak transcription	Pancreas	Pancrea
3	chr6:29948600-29949600	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr6:29948600-29949600	Enhancers	Stomach Mucosa	stomach
5	chr6:29948800-29949800	Enhancers	Rectal Mucosa Donor 29	rectum
6	chr6:29949000-29949600	Flanking Active TSS	Duodenum Mucosa	Duodenum
7	chr6:29949200-29949600	Enhancers	Fetal Intestine Small	intestine
8	chr6:29949400-29953400	Weak transcription	HepG2	liver

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