Variant report

Variant	rs200490
Chromosome Location	chr6:27796935-27796936
allele	A/C
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27110839..27112936-chr6:27796133..27797906,2	K562	blood:
2	chr6:27130895..27132659-chr6:27796327..27798993,2	MCF-7	breast:
3	chr6:27796630..27800125-chr6:28302655..28305022,3	K562	blood:
4	chr6:26105269..26107093-chr6:27796301..27798818,2	MCF-7	breast:
5	chr6:27098287..27103463-chr6:27796109..27800380,7	K562	blood:
6	chr6:27093465..27120217-chr6:27768366..27817187,256	K562	blood:
7	chr6:26025221..26028451-chr6:27796635..27801025,4	K562	blood:
8	chr6:27134929..27137913-chr6:27796376..27797878,2	MCF-7	breast:
9	chr6:26217009..26218913-chr6:27796165..27797886,2	K562	blood:
10	chr1:41706342..41708191-chr6:27795840..27798283,2	K562	blood:
11	chr6:27113131..27119021-chr6:27794877..27801018,12	K562	blood:

No data

Variant related genes	Relation type
ENSG00000265565	Chromatin interaction
ENSG00000124529	Chromatin interaction
ENSG00000198339	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000168274	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000235358	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000010803	Chromatin interaction
ENSG00000124635	Chromatin interaction

Extended variants
information (count: 128 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs1010261	0.88[CHB][hapmap]
rs1015075	0.85[JPT][hapmap]
rs12174918	0.87[ASN][1000 genomes]
rs13193480	0.81[EUR][1000 genomes]
rs13193542	0.81[EUR][1000 genomes]
rs13194781	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs13195728	0.88[EUR][1000 genomes]
rs13199649	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs13199772	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs13199906	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs13202295	0.81[EUR][1000 genomes]
rs13210634	0.91[CEU][hapmap]
rs13212318	0.91[CEU][hapmap]
rs13212651	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs13215275	0.91[CEU][hapmap]
rs13216117	0.81[EUR][1000 genomes]
rs13217620	0.91[CEU][hapmap]
rs13218875	0.91[CEU][hapmap]
rs16867962	1.00[CHB][hapmap]
rs169287	0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs175597	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17693877	1.00[CHB][hapmap]
rs17693963	0.91[CEU][hapmap]
rs17695758	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs17750747	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs17751184	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs17763089	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs183225	1.00[JPT][hapmap]
rs200466	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs200469	0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs200473	1.00[JPT][hapmap]
rs200479	0.88[CHD][hapmap];1.00[JPT][hapmap]
rs200481	1.00[CEU][hapmap];0.94[CHD][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs200482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs200483	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs200484	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs200485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs200488	0.93[ASN][1000 genomes]
rs200489	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs200493	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs200497	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs200498	0.89[ASN][1000 genomes]
rs200499	0.87[ASN][1000 genomes]
rs200501	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs200948	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs200949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs200950	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs200952	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs200953	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs200954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs200964	0.84[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs200965	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[ASN][1000 genomes]
rs200966	0.85[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs200968	0.81[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.82[MEX][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs200973	0.91[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs200974	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs200975	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs200976	0.80[ASN][1000 genomes]
rs200977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs200979	0.82[ASN][1000 genomes]
rs200980	0.82[ASN][1000 genomes]
rs200981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs200983	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs200989	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs200990	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs200992	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs200995	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs200996	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs201002	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2277104	0.91[ASN][1000 genomes]
rs2394001	0.87[ASN][1000 genomes]
rs2747054	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34194357	0.85[EUR][1000 genomes]
rs34295134	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34706883	0.91[CEU][hapmap];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	0.93[ASN][1000 genomes]
rs36116761	0.85[EUR][1000 genomes]
rs370155	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs390764	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs401754	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs401763	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs425335	0.91[CEU][hapmap]
rs45509595	0.85[EUR][1000 genomes]
rs4713122	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4713124	0.87[ASN][1000 genomes]
rs4713127	0.86[ASN][1000 genomes]
rs483143	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs493161	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs494887	0.82[ASN][1000 genomes]
rs557042	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56870390	0.93[ASN][1000 genomes]
rs59015666	0.87[ASN][1000 genomes]
rs61742093	0.81[EUR][1000 genomes]
rs666846	1.00[JPT][hapmap]
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]
rs904142	0.85[JPT][hapmap]
rs9348779	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9357052	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9368531	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9368534	0.95[ASN][1000 genomes]
rs9368535	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9368536	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9368537	0.85[JPT][hapmap]
rs9380018	0.85[ASN][1000 genomes]
rs9380026	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9380028	0.85[JPT][hapmap]
rs9380030	0.85[JPT][hapmap]
rs9393845	0.88[CHB][hapmap]
rs9393854	1.00[CHB][hapmap]
rs9393858	0.91[ASN][1000 genomes]
rs9393862	0.86[ASN][1000 genomes]
rs9468183	0.88[CHB][hapmap]

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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs200490	AL022393.7	cis	Muscle Skeletal	GTEx
rs200490	ZFP57	Cis_chr	lymphoblastoid	RTeQTL
rs200490	HIST1H4J	cis	lymphoblastoid	seeQTL
rs200490	BTN3A2	trans	lymphoblastoid	seeQTL
rs200490	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs200490	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs200490	Hs.158943	cis	multi-tissue	Pritchard

Chromatin state (count:92 , 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	chr6:27791400-27797000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:27792600-27798000	Weak transcription	Fetal Heart	heart
4	chr6:27792800-27798400	Weak transcription	Esophagus	oesophagus
5	chr6:27792800-27798400	Weak transcription	Left Ventricle	heart
6	chr6:27792800-27798400	Weak transcription	Lung	lung
7	chr6:27793000-27798200	Weak transcription	Brain Substantia Nigra	brain
8	chr6:27793200-27797000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:27793200-27797200	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr6:27793200-27797200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr6:27793200-27797400	Weak transcription	Primary B cells from peripheral blood	blood
12	chr6:27793200-27797400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr6:27793200-27797800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr6:27793200-27797800	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr6:27793200-27798200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr6:27793200-27798200	Weak transcription	Right Atrium	heart
17	chr6:27793200-27798200	Weak transcription	Stomach Mucosa	stomach
18	chr6:27793200-27798400	Weak transcription	Colonic Mucosa	Colon
19	chr6:27793400-27797000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr6:27793400-27797200	Weak transcription	Primary hematopoietic stem cells	blood
21	chr6:27793400-27797200	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr6:27793400-27797200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr6:27793400-27797200	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr6:27793400-27797200	Weak transcription	NH-A	brain
25	chr6:27793400-27797400	Weak transcription	NHEK	skin
26	chr6:27793400-27797600	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr6:27793400-27797600	Weak transcription	Duodenum Mucosa	Duodenum
28	chr6:27793400-27797600	Weak transcription	Fetal Lung	lung
29	chr6:27793400-27797600	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr6:27793400-27797800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr6:27793400-27797800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr6:27793400-27797800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr6:27793400-27797800	Weak transcription	Brain Anterior Caudate	brain
34	chr6:27793400-27797800	Weak transcription	Fetal Stomach	stomach
35	chr6:27793400-27797800	Weak transcription	NHDF-Ad	bronchial
36	chr6:27793400-27797800	Weak transcription	Osteobl	bone
37	chr6:27793400-27798000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr6:27793400-27798000	Weak transcription	Fetal Muscle Leg	muscle
39	chr6:27793400-27798200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr6:27793400-27803200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr6:27793600-27797000	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr6:27793600-27797000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr6:27793600-27797000	Weak transcription	Fetal Brain Male	brain
44	chr6:27793600-27797200	Weak transcription	Primary T cells from cord blood	blood
45	chr6:27793600-27797400	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr6:27793600-27797400	Weak transcription	HUVEC	blood vessel
47	chr6:27793600-27797600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr6:27793600-27797600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr6:27793800-27797400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr6:27793800-27798200	Weak transcription	Fetal Muscle Trunk	muscle

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