Variant report

Variant	rs200497
Chromosome Location	chr6:27792640-27792641
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:33)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:33 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:195807417..195809234-chr6:27792326..27795303,2	MCF-7	breast:
2	chr6:26204679..26206586-chr6:27790923..27793517,4	K562	blood:
3	chr6:27112528..27115430-chr6:27791937..27793870,2	MCF-7	breast:
4	chr6:27791848..27794229-chr6:28109901..28113080,3	K562	blood:
5	chr6:26250835..26253676-chr6:27791814..27793929,3	MCF-7	breast:
6	chr16:62119366..62119866-chr6:27792436..27792962,2	HCT-116	colon:
7	chr6:27098197..27103724-chr6:27790239..27793900,13	K562	blood:
8	chr6:26043760..26046185-chr6:27792273..27794565,3	MCF-7	breast:
9	chr6:26025186..26028375-chr6:27792373..27794526,3	MCF-7	breast:
10	chr6:27112528..27118803-chr6:27787647..27794623,16	K562	blood:
11	chr6:26203034..26206484-chr6:27789284..27793104,6	MCF-7	breast:
12	chr6:27103857..27108544-chr6:27789458..27794450,6	K562	blood:
13	chr6:26215488..26220486-chr6:27788576..27794997,7	K562	blood:
14	chr6:27791817..27793378-chr7:558147..559958,2	MCF-7	breast:
15	chr6:26032202..26033763-chr6:27792557..27794069,2	K562	blood:
16	chr6:26156539..26159752-chr6:27789792..27793850,5	MCF-7	breast:
17	chr6:27093465..27120217-chr6:27768366..27817187,256	K562	blood:
18	chr6:27561798..27564734-chr6:27791089..27793910,2	K562	blood:
19	chr6:26194059..26195654-chr6:27792019..27794914,2	MCF-7	breast:
20	chr20:48599056..48599936-chr6:27792484..27793130,2	Hela-S3	cervix:
21	chr2:61763651..61764194-chr6:27791993..27792977,2	Hela-S3	cervix:
22	chr6:26215362..26217924-chr6:27790762..27793250,4	MCF-7	breast:
23	chr6:26197952..26199896-chr6:27792315..27793817,2	MCF-7	breast:
24	chr2:88927237..88927778-chr6:27792368..27793121,2	Hela-S3	cervix:
25	chr6:26122616..26125832-chr6:27791584..27793805,3	K562	blood:
26	chr5:141014554..141017401-chr6:27791505..27793749,2	MCF-7	breast:
27	chr6:26283774..26285764-chr6:27791060..27793861,2	MCF-7	breast:
28	chr5:52405326..52407206-chr6:27791920..27794504,2	K562	blood:
29	chr6:26030055..26033247-chr6:27790818..27793416,3	MCF-7	breast:
30	chr6:27100619..27103482-chr6:27790924..27794224,3	MCF-7	breast:
31	chr6:26122965..26125832-chr6:27791721..27793805,2	K562	blood:
32	chr6:26198756..26200403-chr6:27791864..27793365,2	K562	blood:
33	chr6:27791730..27793405-chr6:28109237..28111401,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000197461	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000168274	Chromatin interaction
ENSG00000164620	Chromatin interaction
ENSG00000234028	Chromatin interaction
ENSG00000082898	Chromatin interaction
ENSG00000247796	Chromatin interaction
ENSG00000234816	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000180573	Chromatin interaction
ENSG00000206671	Chromatin interaction
ENSG00000180596	Chromatin interaction
ENSG00000197459	Chromatin interaction
ENSG00000124216	Chromatin interaction
ENSG00000124693	Chromatin interaction
ENSG00000196226	Chromatin interaction
ENSG00000198315	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000072274	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000198518	Chromatin interaction
ENSG00000196532	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000198339	Chromatin interaction
ENSG00000256316	Chromatin interaction
ENSG00000158406	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000187990	Chromatin interaction
ENSG00000197846	Chromatin interaction
ENSG00000196866	Chromatin interaction
ENSG00000164172	Chromatin interaction
ENSG00000124529	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000197409	Chromatin interaction
ENSG00000171720	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs12174918	0.91[ASN][1000 genomes]
rs13193480	0.81[EUR][1000 genomes]
rs13193542	0.81[EUR][1000 genomes]
rs13194781	0.85[EUR][1000 genomes]
rs13195728	0.88[EUR][1000 genomes]
rs13199649	0.83[EUR][1000 genomes]
rs13199772	0.85[EUR][1000 genomes]
rs13199906	0.85[EUR][1000 genomes]
rs13202295	0.81[EUR][1000 genomes]
rs13212651	0.85[EUR][1000 genomes]
rs13216117	0.81[EUR][1000 genomes]
rs169287	0.84[ASN][1000 genomes]
rs175597	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17695758	0.85[EUR][1000 genomes]
rs17750747	0.81[EUR][1000 genomes]
rs17751184	0.88[EUR][1000 genomes]
rs17763089	0.85[EUR][1000 genomes]
rs183225	0.83[ASN][1000 genomes]
rs200466	0.83[ASN][1000 genomes]
rs200469	0.81[ASN][1000 genomes]
rs200471	0.83[ASN][1000 genomes]
rs200473	0.83[ASN][1000 genomes]
rs200478	0.83[ASN][1000 genomes]
rs200479	0.83[ASN][1000 genomes]
rs200481	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs200482	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs200483	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs200484	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs200485	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs200488	0.89[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs200489	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs200490	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs200493	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs200498	0.98[ASN][1000 genomes]
rs200499	0.95[ASN][1000 genomes]
rs200501	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs200948	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs200949	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs200950	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs200952	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs200953	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs200954	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs200964	0.84[ASN][1000 genomes]
rs200965	0.86[ASN][1000 genomes]
rs200966	0.84[ASN][1000 genomes]
rs200968	0.86[ASN][1000 genomes]
rs200973	0.84[ASN][1000 genomes]
rs200974	0.86[ASN][1000 genomes]
rs200976	0.84[ASN][1000 genomes]
rs200977	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs200979	0.86[ASN][1000 genomes]
rs200980	0.86[ASN][1000 genomes]
rs200981	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs200983	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs200989	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs200990	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs200992	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs200995	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs200996	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs201002	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2277104	1.00[ASN][1000 genomes]
rs2394001	0.91[ASN][1000 genomes]
rs2747054	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34194357	0.85[EUR][1000 genomes]
rs34295134	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34706883	0.88[EUR][1000 genomes]
rs34718920	0.88[EUR][1000 genomes]
rs34788973	0.81[EUR][1000 genomes]
rs35037868	0.81[EUR][1000 genomes]
rs35501037	0.81[EUR][1000 genomes]
rs35819751	0.85[EUR][1000 genomes]
rs36101351	0.81[EUR][1000 genomes]
rs36108923	0.98[ASN][1000 genomes]
rs36116761	0.85[EUR][1000 genomes]
rs370155	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs390764	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs401754	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs401763	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs45509595	0.85[EUR][1000 genomes]
rs4713122	0.91[ASN][1000 genomes]
rs4713124	0.91[ASN][1000 genomes]
rs4713127	0.91[ASN][1000 genomes]
rs483143	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs493161	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs494887	0.86[ASN][1000 genomes]
rs557042	0.85[AFR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56870390	0.98[ASN][1000 genomes]
rs59015666	0.91[ASN][1000 genomes]
rs61742093	0.81[EUR][1000 genomes]
rs666846	0.83[ASN][1000 genomes]
rs66868086	0.85[EUR][1000 genomes]
rs67040724	0.81[EUR][1000 genomes]
rs67101035	0.88[EUR][1000 genomes]
rs71559050	0.88[EUR][1000 genomes]
rs71559054	0.81[EUR][1000 genomes]
rs72847313	0.81[EUR][1000 genomes]
rs9348779	0.93[ASN][1000 genomes]
rs9357052	0.91[ASN][1000 genomes]
rs9368531	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9368534	0.95[ASN][1000 genomes]
rs9368535	0.93[ASN][1000 genomes]
rs9368536	0.93[ASN][1000 genomes]
rs9380018	0.89[ASN][1000 genomes]
rs9380026	0.91[ASN][1000 genomes]
rs9393858	0.95[ASN][1000 genomes]
rs9393862	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases
3	nsv1017440	chr6:27734824-27864277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	370 gene(s)	inside rSNPs	diseases
4	nsv1022173	chr6:27734824-27959408	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
5	nsv883512	chr6:27748631-27969004	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs200497	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs200497	ZFP57	Cis_chr	lymphoblastoid	RTeQTL
rs200497	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27791000-27793000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr6:27791200-27792800	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr6:27791200-27792800	Active TSS	Muscle Satellite Cultured Cells	--
4	chr6:27791200-27792800	Active TSS	Fetal Brain Male	brain
5	chr6:27791200-27793000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:27791200-27793000	Active TSS	Primary T regulatory cells fromperipheralblood	blood
7	chr6:27791200-27793000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:27791200-27793000	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
9	chr6:27791200-27793000	Active TSS	Fetal Intestine Large	intestine
10	chr6:27791200-27793000	Active TSS	Rectal Mucosa Donor 31	rectum
11	chr6:27791200-27793200	Active TSS	Colonic Mucosa	Colon
12	chr6:27791200-27793200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
13	chr6:27791200-27793200	Active TSS	Fetal Lung	lung
14	chr6:27791200-27793200	Active TSS	Rectal Smooth Muscle	rectum
15	chr6:27791200-27793200	Active TSS	Right Atrium	heart
16	chr6:27791200-27793400	Active TSS	Brain Anterior Caudate	brain
17	chr6:27791200-27793400	Active TSS	Fetal Muscle Leg	muscle
18	chr6:27791200-27793400	Active TSS	Fetal Stomach	stomach
19	chr6:27791200-27793400	Active TSS	Rectal Mucosa Donor 29	rectum
20	chr6:27791200-27793400	Active TSS	NHLF	lung
21	chr6:27791200-27793600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr6:27791200-27793600	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr6:27791200-27793600	Active TSS	GM12878-XiMat	blood
24	chr6:27791200-27793800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr6:27791200-27794000	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr6:27791200-27794000	Active TSS	Fetal Intestine Small	intestine
27	chr6:27791200-27794600	Active TSS	Fetal Thymus	thymus
28	chr6:27791200-27794600	Active TSS	Thymus	Thymus
29	chr6:27791200-27798000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr6:27791400-27792800	Active TSS	Primary T cells from cord blood	blood
31	chr6:27791400-27792800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr6:27791400-27792800	Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr6:27791400-27792800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
34	chr6:27791400-27792800	Active TSS	Duodenum Mucosa	Duodenum
35	chr6:27791400-27792800	Active TSS	Esophagus	oesophagus
36	chr6:27791400-27792800	Active TSS	Ovary	ovary
37	chr6:27791400-27792800	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
38	chr6:27791400-27793000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr6:27791400-27793000	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr6:27791400-27793000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr6:27791400-27793000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr6:27791400-27793000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr6:27791400-27793000	Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr6:27791400-27793000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
45	chr6:27791400-27793000	Active TSS	Fetal Kidney	kidney
46	chr6:27791400-27793000	Active TSS	Placenta Amnion	Placenta Amnion
47	chr6:27791400-27793000	Active TSS	Right Ventricle	heart
48	chr6:27791400-27793000	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
49	chr6:27791400-27793200	Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr6:27791400-27793200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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