Variant report

Variant	rs200493
Chromosome Location	chr6:27795418-27795419
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:27093465..27120217-chr6:27768366..27817187,256	K562	blood:
2	chr6:27113131..27119021-chr6:27794877..27801018,12	K562	blood:

Variant related genes	Relation type
ENSG00000196787	Chromatin interaction
ENSG00000198339	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000184825	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs13194781	0.82[EUR][1000 genomes]
rs13195728	0.85[EUR][1000 genomes]
rs13199649	0.80[EUR][1000 genomes]
rs13199772	0.82[EUR][1000 genomes]
rs13199906	0.82[EUR][1000 genomes]
rs13212651	0.82[EUR][1000 genomes]
rs13218875	0.80[EUR][1000 genomes]
rs175597	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17695758	0.82[EUR][1000 genomes]
rs17751184	0.85[EUR][1000 genomes]
rs17763089	0.82[EUR][1000 genomes]
rs200481	0.95[EUR][1000 genomes]
rs200482	0.93[EUR][1000 genomes]
rs200483	0.95[EUR][1000 genomes]
rs200484	0.84[EUR][1000 genomes]
rs200485	0.95[EUR][1000 genomes]
rs200488	0.82[ASN][1000 genomes]
rs200489	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs200490	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs200497	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs200501	0.95[EUR][1000 genomes]
rs200948	0.92[EUR][1000 genomes]
rs200949	0.84[EUR][1000 genomes]
rs200950	0.92[EUR][1000 genomes]
rs200952	0.92[EUR][1000 genomes]
rs200953	0.90[EUR][1000 genomes]
rs200954	0.92[EUR][1000 genomes]
rs200977	0.92[EUR][1000 genomes]
rs200981	0.90[EUR][1000 genomes]
rs200983	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs200989	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs200990	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs200992	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs200995	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs200996	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs201002	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2747054	0.95[EUR][1000 genomes]
rs34194357	0.82[EUR][1000 genomes]
rs34295134	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34706883	0.85[EUR][1000 genomes]
rs34718920	0.85[EUR][1000 genomes]
rs35819751	0.82[EUR][1000 genomes]
rs36108923	0.82[ASN][1000 genomes]
rs36116761	0.82[EUR][1000 genomes]
rs370155	0.93[EUR][1000 genomes]
rs390764	0.95[EUR][1000 genomes]
rs401754	0.95[EUR][1000 genomes]
rs45509595	0.82[EUR][1000 genomes]
rs483143	0.90[EUR][1000 genomes]
rs493161	0.92[EUR][1000 genomes]
rs557042	0.92[EUR][1000 genomes]
rs56870390	0.82[ASN][1000 genomes]
rs66868086	0.82[EUR][1000 genomes]
rs67101035	0.85[EUR][1000 genomes]
rs71559050	0.85[EUR][1000 genomes]
rs9368531	0.95[EUR][1000 genomes]
rs9368534	0.84[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
rs200493	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs200493	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs200493	ZFP57	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27791200-27798000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:27791400-27795800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr6:27791400-27797000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:27791600-27796600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:27792600-27798000	Weak transcription	Fetal Heart	heart
6	chr6:27792800-27798400	Weak transcription	Esophagus	oesophagus
7	chr6:27792800-27798400	Weak transcription	Left Ventricle	heart
8	chr6:27792800-27798400	Weak transcription	Lung	lung
9	chr6:27793000-27798200	Weak transcription	Brain Substantia Nigra	brain
10	chr6:27793200-27796400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr6:27793200-27797000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr6:27793200-27797200	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr6:27793200-27797200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr6:27793200-27797400	Weak transcription	Primary B cells from peripheral blood	blood
15	chr6:27793200-27797400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr6:27793200-27797800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr6:27793200-27797800	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr6:27793200-27798200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:27793200-27798200	Weak transcription	Right Atrium	heart
20	chr6:27793200-27798200	Weak transcription	Stomach Mucosa	stomach
21	chr6:27793200-27798400	Weak transcription	Colonic Mucosa	Colon
22	chr6:27793400-27796600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr6:27793400-27796800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr6:27793400-27796800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr6:27793400-27796800	Weak transcription	HepG2	liver
26	chr6:27793400-27797000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr6:27793400-27797200	Weak transcription	Primary hematopoietic stem cells	blood
28	chr6:27793400-27797200	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr6:27793400-27797200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr6:27793400-27797200	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr6:27793400-27797200	Weak transcription	NH-A	brain
32	chr6:27793400-27797400	Weak transcription	NHEK	skin
33	chr6:27793400-27797600	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr6:27793400-27797600	Weak transcription	Duodenum Mucosa	Duodenum
35	chr6:27793400-27797600	Weak transcription	Fetal Lung	lung
36	chr6:27793400-27797600	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr6:27793400-27797800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr6:27793400-27797800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr6:27793400-27797800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr6:27793400-27797800	Weak transcription	Brain Anterior Caudate	brain
41	chr6:27793400-27797800	Weak transcription	Fetal Stomach	stomach
42	chr6:27793400-27797800	Weak transcription	NHDF-Ad	bronchial
43	chr6:27793400-27797800	Weak transcription	Osteobl	bone
44	chr6:27793400-27798000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr6:27793400-27798000	Weak transcription	Fetal Muscle Leg	muscle
46	chr6:27793400-27798200	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr6:27793400-27803200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr6:27793600-27796200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr6:27793600-27796400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr6:27793600-27796600	Weak transcription	GM12878-XiMat	blood

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