Variant report

Variant	rs200488
Chromosome Location	chr6:27799045-27799046
allele	A/C/G/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: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	chr6:27796630..27800125-chr6:28302655..28305022,3	K562	blood:
2	chr1:150121553..150123075-chr6:27798165..27799927,2	MCF-7	breast:
3	chr6:27798954..27801175-chr6:28191953..28194580,2	K562	blood:
4	chr6:27797129..27799263-chr6:28192997..28194501,2	K562	blood:
5	chr6:27104100..27108145-chr6:27797427..27800059,3	K562	blood:
6	chr6:26155325..26157964-chr6:27797146..27799688,3	MCF-7	breast:
7	chr6:27797717..27799808-chr9:127629757..127631967,2	K562	blood:
8	chr6:26187875..26189403-chr6:27797113..27800006,2	MCF-7	breast:
9	chr6:26053058..26056960-chr6:27797302..27800295,3	MCF-7	breast:
10	chr6:27798350..27799895-chr6:34855095..34857385,2	K562	blood:
11	chr6:27796980..27799834-chr6:28103780..28105751,2	K562	blood:
12	chr6:27213809..27216585-chr6:27797582..27799196,2	K562	blood:
13	chr6:27098287..27103463-chr6:27796109..27800380,7	K562	blood:
14	chr6:27093465..27120217-chr6:27768366..27817187,256	K562	blood:
15	chr6:26122973..26125036-chr6:27798042..27800567,2	MCF-7	breast:
16	chr6:27798054..27799666-chr7:102036106..102037763,2	MCF-7	breast:
17	chr6:27798199..27799834-chr6:28104251..28105914,2	K562	blood:
18	chr6:27782776..27783687-chr6:27798847..27799701,2	NB4	blood:
19	chr13:74708317..74709142-chr6:27798611..27799298,2	Hela-S3	cervix:
20	chr6:26025221..26028451-chr6:27796635..27801025,4	K562	blood:
21	chr14:23387918..23388718-chr6:27798376..27799339,2	Hela-S3	cervix:
22	chr6:26025403..26028129-chr6:27797100..27800385,4	MCF-7	breast:
23	chr6:27113131..27119021-chr6:27794877..27801018,12	K562	blood:
24	chr6:27798534..27801249-chrX:16803484..16805157,2	MCF-7	breast:
25	chr14:93673121..93674052-chr6:27798856..27799361,2	Hela-S3	cervix:
26	chr10:17270443..17271172-chr6:27798257..27799134,2	Hela-S3	cervix:
27	chr6:27798268..27799134-chr6:91006178..91006975,2	HCT-116	colon:
28	chr6:26251146..26253311-chr6:27798112..27799639,2	MCF-7	breast:
29	chr6:27798625..27800434-chr6:28302917..28305015,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000168298	Chromatin interaction
ENSG00000196374	Chromatin interaction
ENSG00000124529	Chromatin interaction
ENSG00000086712	Chromatin interaction
ENSG00000026025	Chromatin interaction
ENSG00000180596	Chromatin interaction
ENSG00000112812	Chromatin interaction
ENSG00000197903	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000197459	Chromatin interaction
ENSG00000118922	Chromatin interaction
ENSG00000064995	Chromatin interaction
ENSG00000100461	Chromatin interaction
ENSG00000128563	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000198339	Chromatin interaction
ENSG00000187837	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000170270	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000237054	Chromatin interaction
ENSG00000012963	Chromatin interaction
ENSG00000023902	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000112182	Chromatin interaction
ENSG00000180573	Chromatin interaction
ENSG00000188987	Chromatin interaction
ENSG00000064999	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000136950	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs12174918	0.93[ASN][1000 genomes]
rs169287	0.87[ASN][1000 genomes]
rs175597	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs183225	0.85[ASN][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	0.91[ASN][1000 genomes]
rs200482	0.91[ASN][1000 genomes]
rs200483	0.93[ASN][1000 genomes]
rs200484	0.87[ASN][1000 genomes]
rs200485	0.91[ASN][1000 genomes]
rs200489	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs200490	0.93[ASN][1000 genomes]
rs200493	0.82[ASN][1000 genomes]
rs200497	0.89[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs200498	0.95[ASN][1000 genomes]
rs200499	0.93[ASN][1000 genomes]
rs200501	0.95[ASN][1000 genomes]
rs200948	0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs200949	0.93[ASN][1000 genomes]
rs200950	0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs200952	0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs200953	0.93[ASN][1000 genomes]
rs200954	0.88[AFR][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	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs200979	0.89[ASN][1000 genomes]
rs200980	0.89[ASN][1000 genomes]
rs200981	0.93[ASN][1000 genomes]
rs200983	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs200989	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs200990	0.98[ASN][1000 genomes]
rs200992	0.98[ASN][1000 genomes]
rs200995	1.00[ASN][1000 genomes]
rs200996	1.00[ASN][1000 genomes]
rs201002	0.98[ASN][1000 genomes]
rs2277104	0.98[ASN][1000 genomes]
rs2394001	0.93[ASN][1000 genomes]
rs2747054	0.98[ASN][1000 genomes]
rs34295134	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs36108923	1.00[ASN][1000 genomes]
rs370155	0.93[ASN][1000 genomes]
rs390764	0.98[ASN][1000 genomes]
rs401754	0.98[ASN][1000 genomes]
rs401763	0.95[ASN][1000 genomes]
rs4236045	0.86[EUR][1000 genomes]
rs4713122	0.93[ASN][1000 genomes]
rs4713124	0.93[ASN][1000 genomes]
rs4713127	0.93[ASN][1000 genomes]
rs483143	0.84[ASN][1000 genomes]
rs493161	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs494887	0.89[ASN][1000 genomes]
rs557042	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs56870390	1.00[ASN][1000 genomes]
rs59015666	0.93[ASN][1000 genomes]
rs666846	0.85[ASN][1000 genomes]
rs9348779	0.95[ASN][1000 genomes]
rs9357052	0.93[ASN][1000 genomes]
rs9368531	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

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27793400-27803200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:27797200-27799600	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:27797200-27799600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:27797200-27799600	Active TSS	Brain Germinal Matrix	brain
5	chr6:27797200-27799800	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr6:27797400-27799200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:27797400-27799200	Active TSS	A549	lung
8	chr6:27797400-27799400	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr6:27797400-27799600	Active TSS	H1 Cell Line	embryonic stem cell
10	chr6:27797400-27799600	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr6:27797400-27799800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:27797600-27799600	Active TSS	H9 Cell Line	embryonic stem cell
13	chr6:27797600-27799600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:27797600-27799600	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr6:27797600-27799600	Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr6:27797600-27799600	Active TSS	Thymus	Thymus
17	chr6:27797600-27799800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr6:27797600-27799800	Active TSS	Rectal Smooth Muscle	rectum
19	chr6:27797600-27799800	Active TSS	HMEC	breast
20	chr6:27797600-27799800	Active TSS	NHLF	lung
21	chr6:27797800-27799200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr6:27797800-27799200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:27797800-27799600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr6:27797800-27799800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:27797800-27799800	Active TSS	Brain Anterior Caudate	brain
26	chr6:27797800-27799800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr6:27797800-27799800	Active TSS	Fetal Intestine Large	intestine
28	chr6:27797800-27799800	Active TSS	Stomach Smooth Muscle	stomach
29	chr6:27797800-27800200	Active TSS	GM12878-XiMat	blood
30	chr6:27798000-27799200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr6:27798000-27799600	Active TSS	iPS-18 Cell Line	embryonic stem cell
32	chr6:27798000-27799600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr6:27798000-27799800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr6:27798000-27799800	Active TSS	Fetal Thymus	thymus
35	chr6:27798000-27799800	Active TSS	NHDF-Ad	bronchial
36	chr6:27798200-27799200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr6:27798200-27799200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr6:27798200-27799200	Active TSS	Sigmoid Colon	Sigmoid Colon
39	chr6:27798200-27799600	Active TSS	HUES48 Cell Line	embryonic stem cell
40	chr6:27798200-27799600	Active TSS	Brain Substantia Nigra	brain
41	chr6:27798200-27799600	Active TSS	Hela-S3	cervix
42	chr6:27798200-27799600	Active TSS	HSMM	muscle
43	chr6:27798200-27799800	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr6:27798200-27799800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
45	chr6:27798200-27799800	Active TSS	Fetal Muscle Trunk	muscle
46	chr6:27798400-27799200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr6:27798400-27799400	Transcr. at gene 5' and 3'	Right Atrium	heart
48	chr6:27798400-27799600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr6:27798400-27799600	Active TSS	Primary hematopoietic stem cells short term culture	blood
50	chr6:27798400-27799600	Active TSS	Aorta	Aorta

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