Variant report

Variant	rs200489
Chromosome Location	chr6:27798257-27798258
allele	A/G
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:29)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:29 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27130895..27132659-chr6:27796327..27798993,2	MCF-7	breast:
2	chr6:27796630..27800125-chr6:28302655..28305022,3	K562	blood:
3	chr1:150121553..150123075-chr6:27798165..27799927,2	MCF-7	breast:
4	chr6:27797129..27799263-chr6:28192997..28194501,2	K562	blood:
5	chr6:27104100..27108145-chr6:27797427..27800059,3	K562	blood:
6	chr6:27144382..27146185-chr6:27797360..27798889,2	MCF-7	breast:
7	chr6:26155325..26157964-chr6:27797146..27799688,3	MCF-7	breast:
8	chr6:26249639..26251537-chr6:27797194..27798827,2	MCF-7	breast:
9	chr6:27797717..27799808-chr9:127629757..127631967,2	K562	blood:
10	chr6:26105269..26107093-chr6:27796301..27798818,2	MCF-7	breast:
11	chr6:26187875..26189403-chr6:27797113..27800006,2	MCF-7	breast:
12	chr6:26053058..26056960-chr6:27797302..27800295,3	MCF-7	breast:
13	chr6:27796980..27799834-chr6:28103780..28105751,2	K562	blood:
14	chr6:27213809..27216585-chr6:27797582..27799196,2	K562	blood:
15	chr6:27797159..27798965-chr6:28302393..28304986,2	MCF-7	breast:
16	chr6:27098287..27103463-chr6:27796109..27800380,7	K562	blood:
17	chr6:27093465..27120217-chr6:27768366..27817187,256	K562	blood:
18	chr6:26122973..26125036-chr6:27798042..27800567,2	MCF-7	breast:
19	chr6:27798054..27799666-chr7:102036106..102037763,2	MCF-7	breast:
20	chr6:27798199..27799834-chr6:28104251..28105914,2	K562	blood:
21	chr6:26025221..26028451-chr6:27796635..27801025,4	K562	blood:
22	chr6:26223975..26226167-chr6:27797059..27798988,2	MCF-7	breast:
23	chr6:26025403..26028129-chr6:27797100..27800385,4	MCF-7	breast:
24	chr1:41706342..41708191-chr6:27795840..27798283,2	K562	blood:
25	chr6:27113131..27119021-chr6:27794877..27801018,12	K562	blood:
26	chr10:17270443..17271172-chr6:27798257..27799134,2	Hela-S3	cervix:
27	chr6:26278895..26281464-chr6:27797279..27798878,2	MCF-7	breast:
28	chr6:27797788..27798731-chr6:43395476..43396097,2	HCT-116	colon:
29	chr6:26251146..26253311-chr6:27798112..27799639,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000124635	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000112812	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000198339	Chromatin interaction
ENSG00000187837	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000023902	Chromatin interaction
ENSG00000196966	Chromatin interaction
ENSG00000235358	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000010803	Chromatin interaction
ENSG00000180573	Chromatin interaction
ENSG00000197459	Chromatin interaction
ENSG00000256316	Chromatin interaction
ENSG00000188987	Chromatin interaction
ENSG00000124529	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000128563	Chromatin interaction
ENSG00000180596	Chromatin interaction
ENSG00000124574	Chromatin interaction
ENSG00000136950	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000026025	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs12174918	0.93[ASN][1000 genomes]
rs13193480	0.83[EUR][1000 genomes]
rs13193542	0.83[EUR][1000 genomes]
rs13194781	0.86[EUR][1000 genomes]
rs13195728	0.90[EUR][1000 genomes]
rs13199649	0.84[EUR][1000 genomes]
rs13199772	0.86[EUR][1000 genomes]
rs13199906	0.86[EUR][1000 genomes]
rs13202291	0.81[EUR][1000 genomes]
rs13202295	0.83[EUR][1000 genomes]
rs13212651	0.86[EUR][1000 genomes]
rs13216117	0.83[EUR][1000 genomes]
rs169287	0.87[ASN][1000 genomes]
rs175597	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17695758	0.86[EUR][1000 genomes]
rs17750747	0.83[EUR][1000 genomes]
rs17751184	0.90[EUR][1000 genomes]
rs17763089	0.86[EUR][1000 genomes]
rs183225	0.85[ASN][1000 genomes]
rs188015	0.81[EUR][1000 genomes]
rs200466	0.85[ASN][1000 genomes]
rs200469	0.83[ASN][1000 genomes]
rs200471	0.85[ASN][1000 genomes]
rs200473	0.85[ASN][1000 genomes]
rs200478	0.85[ASN][1000 genomes]
rs200479	0.85[ASN][1000 genomes]
rs200481	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs200482	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs200483	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs200484	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs200485	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs200488	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs200490	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs200493	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs200497	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs200498	0.95[ASN][1000 genomes]
rs200499	0.93[ASN][1000 genomes]
rs200501	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs200948	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs200949	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs200950	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs200952	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs200953	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs200954	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs200964	0.87[ASN][1000 genomes]
rs200965	0.89[ASN][1000 genomes]
rs200966	0.87[ASN][1000 genomes]
rs200968	0.89[ASN][1000 genomes]
rs200973	0.87[ASN][1000 genomes]
rs200974	0.89[ASN][1000 genomes]
rs200975	0.80[ASN][1000 genomes]
rs200976	0.87[ASN][1000 genomes]
rs200977	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs200979	0.89[ASN][1000 genomes]
rs200980	0.89[ASN][1000 genomes]
rs200981	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs200983	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200989	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200990	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs200992	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs200995	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200996	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs201002	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2277104	0.98[ASN][1000 genomes]
rs2394001	0.93[ASN][1000 genomes]
rs2747054	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28360499	0.81[EUR][1000 genomes]
rs34194357	0.86[EUR][1000 genomes]
rs34295134	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34706883	0.90[EUR][1000 genomes]
rs34718920	0.90[EUR][1000 genomes]
rs34788973	0.83[EUR][1000 genomes]
rs35037868	0.83[EUR][1000 genomes]
rs35501037	0.83[EUR][1000 genomes]
rs35819751	0.86[EUR][1000 genomes]
rs36101351	0.83[EUR][1000 genomes]
rs36108923	1.00[ASN][1000 genomes]
rs36116761	0.86[EUR][1000 genomes]
rs370155	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs390764	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs401754	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs401763	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs45509595	0.86[EUR][1000 genomes]
rs4713122	0.93[ASN][1000 genomes]
rs4713124	0.93[ASN][1000 genomes]
rs4713127	0.93[ASN][1000 genomes]
rs483143	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs493161	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs494887	0.89[ASN][1000 genomes]
rs557042	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56870390	1.00[ASN][1000 genomes]
rs59015666	0.93[ASN][1000 genomes]
rs61742093	0.83[EUR][1000 genomes]
rs666846	0.85[ASN][1000 genomes]
rs66868086	0.86[EUR][1000 genomes]
rs67040724	0.83[EUR][1000 genomes]
rs67101035	0.90[EUR][1000 genomes]
rs71559050	0.90[EUR][1000 genomes]
rs71559054	0.83[EUR][1000 genomes]
rs72847313	0.83[EUR][1000 genomes]
rs9348779	0.95[ASN][1000 genomes]
rs9357052	0.93[ASN][1000 genomes]
rs9368531	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9368534	0.98[ASN][1000 genomes]
rs9368535	0.95[ASN][1000 genomes]
rs9368536	0.95[ASN][1000 genomes]
rs9380018	0.91[ASN][1000 genomes]
rs9380026	0.93[ASN][1000 genomes]
rs9393858	0.98[ASN][1000 genomes]
rs9393862	0.93[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
rs200489	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs200489	ZFP57	Cis_chr	lymphoblastoid	RTeQTL
rs200489	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27792800-27798400	Weak transcription	Esophagus	oesophagus
2	chr6:27792800-27798400	Weak transcription	Left Ventricle	heart
3	chr6:27792800-27798400	Weak transcription	Lung	lung
4	chr6:27793200-27798400	Weak transcription	Colonic Mucosa	Colon
5	chr6:27793400-27803200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:27794600-27798400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr6:27794600-27798400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr6:27795600-27798400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr6:27796800-27798600	Transcr. at gene 5' and 3'	K562	blood
10	chr6:27797000-27799000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr6:27797200-27798600	Flanking Active TSS	Dnd41	blood
12	chr6:27797200-27799600	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr6:27797200-27799600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr6:27797200-27799600	Active TSS	Brain Germinal Matrix	brain
15	chr6:27797200-27799800	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr6:27797400-27798600	Weak transcription	Small Intestine	intestine
17	chr6:27797400-27799200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr6:27797400-27799200	Active TSS	A549	lung
19	chr6:27797400-27799400	Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr6:27797400-27799600	Active TSS	H1 Cell Line	embryonic stem cell
21	chr6:27797400-27799600	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr6:27797400-27799800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:27797600-27798400	Weak transcription	Gastric	stomach
24	chr6:27797600-27798600	Flanking Active TSS	Primary B cells from cord blood	blood
25	chr6:27797600-27798600	Flanking Active TSS	Fetal Brain Female	brain
26	chr6:27797600-27798800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr6:27797600-27798800	Flanking Active TSS	NH-A	brain
28	chr6:27797600-27799000	Flanking Active TSS	Primary hematopoietic stem cells	blood
29	chr6:27797600-27799000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr6:27797600-27799000	Flanking Active TSS	Duodenum Mucosa	Duodenum
31	chr6:27797600-27799600	Active TSS	H9 Cell Line	embryonic stem cell
32	chr6:27797600-27799600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:27797600-27799600	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr6:27797600-27799600	Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr6:27797600-27799600	Active TSS	Thymus	Thymus
36	chr6:27797600-27799800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr6:27797600-27799800	Active TSS	Rectal Smooth Muscle	rectum
38	chr6:27797600-27799800	Active TSS	HMEC	breast
39	chr6:27797600-27799800	Active TSS	NHLF	lung
40	chr6:27797800-27798400	Active TSS	Rectal Mucosa Donor 31	rectum
41	chr6:27797800-27798600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr6:27797800-27798600	Flanking Active TSS	Fetal Kidney	kidney
43	chr6:27797800-27798800	Flanking Active TSS	Primary T cells from cord blood	blood
44	chr6:27797800-27798800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
45	chr6:27797800-27798800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr6:27797800-27799000	Flanking Active TSS	Primary B cells from peripheral blood	blood
47	chr6:27797800-27799000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
48	chr6:27797800-27799000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr6:27797800-27799000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
50	chr6:27797800-27799000	Flanking Active TSS	HUVEC	blood vessel

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