Variant report

Variant	rs2246198
Chromosome Location	chr6:29945602-29945603
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	chr6:29855991..29858588-chr6:29944087..29945954,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230521	Chromatin interaction

Extended variants
information (count: 168 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:145)

rs_ID	r²[population]
rs1048412	0.82[AFR][1000 genomes]
rs17187210	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2074479	0.82[AFR][1000 genomes]
rs2074480	0.82[AFR][1000 genomes]
rs2074482	0.82[AFR][1000 genomes]
rs2246199	0.82[AMR][1000 genomes]
rs2246638	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2286405	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2301753	0.82[AFR][1000 genomes]
rs2301754	0.82[AFR][1000 genomes]
rs2394254	0.80[ASN][1000 genomes]
rs2394256	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2394257	0.81[ASN][1000 genomes]
rs2571431	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2735071	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2894002	0.89[ASN][1000 genomes]
rs3734835	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs3765604	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs3765606	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs3869067	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs3869068	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs3893530	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4448133	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6902691	0.85[ASN][1000 genomes]
rs6905157	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6910507	0.92[ASN][1000 genomes]
rs6910517	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6910898	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6911279	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6911467	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6911737	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6912080	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6912154	0.89[ASN][1000 genomes]
rs6912877	0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6919617	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6922640	0.80[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6926792	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6930993	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6931776	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6941318	0.80[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7738475	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7742417	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7742871	0.80[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7746866	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7750514	0.80[ASN][1000 genomes]
rs7751116	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7758512	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7760299	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7768179	0.80[ASN][1000 genomes]
rs9260951	0.94[ASN][1000 genomes]
rs9260959	0.91[ASN][1000 genomes]
rs9260960	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9260961	0.80[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9260963	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9260964	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9260965	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9260966	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9260967	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9260968	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9260970	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9260971	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9260972	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9260974	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9260975	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9260977	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9260978	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9260979	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9260980	0.89[ASN][1000 genomes]
rs9260982	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9260987	0.92[ASN][1000 genomes]
rs9260990	0.87[ASN][1000 genomes]
rs9260992	0.81[ASN][1000 genomes]
rs9260994	0.92[ASN][1000 genomes]
rs9260995	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9260996	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9260999	0.80[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs9261000	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9261001	0.85[ASN][1000 genomes]
rs9261003	0.92[ASN][1000 genomes]
rs9261004	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9261008	0.91[ASN][1000 genomes]
rs9261009	0.92[ASN][1000 genomes]
rs9261010	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9261012	0.85[ASN][1000 genomes]
rs9261013	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9261015	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9261016	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9261020	0.89[ASN][1000 genomes]
rs9261022	0.89[ASN][1000 genomes]
rs9261023	0.89[ASN][1000 genomes]
rs9261024	0.89[ASN][1000 genomes]
rs9261026	0.89[ASN][1000 genomes]
rs9261031	0.80[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9261033	0.80[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs9261049	0.80[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9261060	0.87[ASN][1000 genomes]
rs9261074	0.88[ASN][1000 genomes]
rs9261103	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9261105	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9261110	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9261111	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9261113	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9261115	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9261116	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9261128	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs9261129	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9261137	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9261145	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9261149	0.80[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9261150	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9261154	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9261162	0.85[ASN][1000 genomes]
rs9261163	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9261170	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9261174	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9261180	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9261183	0.80[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9261185	0.80[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9261186	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9261187	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9261188	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9261189	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9261195	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9261198	0.85[ASN][1000 genomes]
rs9261199	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9261200	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9261201	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9261204	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9261205	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9261206	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9261209	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9261210	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9261216	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9261217	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9261221	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9261222	0.80[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9261291	0.82[AFR][1000 genomes]
rs9261292	0.82[AFR][1000 genomes]
rs9261294	0.82[AFR][1000 genomes]
rs9261295	0.82[AFR][1000 genomes]
rs9261297	0.82[AFR][1000 genomes]
rs9261298	0.82[AFR][1000 genomes]
rs9261299	0.82[AFR][1000 genomes]
rs9261300	0.82[AFR][1000 genomes]
rs9261302	0.82[AFR][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	nsv511863	chr6:29945557-29948665	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2246198	ZNRD1	cis	multi-tissue	Pritchard
rs2246198	C6orf12	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29945000-29945800	Bivalent Enhancer	Fetal Heart	heart
2	chr6:29945000-29945800	Flanking Active TSS	K562	blood
3	chr6:29945200-29945800	Enhancers	Liver	Liver
4	chr6:29945200-29948600	Weak transcription	Small Intestine	intestine
5	chr6:29945200-29948600	Weak transcription	Spleen	Spleen
6	chr6:29945400-29945800	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr6:29945400-29945800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:29945400-29945800	Enhancers	Fetal Intestine Small	intestine
9	chr6:29945400-29945800	Enhancers	Pancreatic Islets	Pancreatic Islet
10	chr6:29945400-29945800	Enhancers	A549	lung
11	chr6:29945400-29948800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr6:29945400-29950200	Weak transcription	Right Atrium	heart
13	chr6:29945600-29945800	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr6:29945600-29945800	Enhancers	HepG2	liver
15	chr6:29945600-29948000	Weak transcription	Colonic Mucosa	Colon
16	chr6:29945600-29948600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr6:29945600-29948600	Weak transcription	Stomach Mucosa	stomach
18	chr6:29945600-29948800	Weak transcription	Duodenum Mucosa	Duodenum
19	chr6:29945600-29966400	Weak transcription	Pancreas	Pancrea

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