Variant report

Variant	rs16888130
Chromosome Location	chr6:56574180-56574181
allele	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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:56573561..56574379-chr6:56622555..56623519,3	MCF-7	breast:
2	chr6:56569145..56571634-chr6:56573957..56575917,2	MCF-7	breast:
3	chr6:56572610..56574602-chr6:56715205..56717521,2	MCF-7	breast:
4	chr6:56565438..56567877-chr6:56572534..56575262,2	K562	blood:
5	chr6:56573945..56574696-chr6:56715916..56716847,2	MCF-7	breast:
6	chr6:56573542..56574688-chr6:56622197..56623128,5	MCF-7	breast:
7	chr6:56573656..56574382-chr6:56628597..56629104,2	MCF-7	breast:
8	chr6:56572377..56575419-chr6:56576421..56579962,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000151914	Chromatin interaction

Extended variants
information (count: 136 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs1024196	1.00[ASN][1000 genomes]
rs10498811	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs11961141	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11961342	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11966986	1.00[ASN][1000 genomes]
rs11967796	1.00[ASN][1000 genomes]
rs11968575	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11970410	0.90[ASN][1000 genomes]
rs13191164	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13192037	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs13192478	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13192567	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13196211	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs13198399	0.85[EUR][1000 genomes]
rs13198938	0.85[EUR][1000 genomes]
rs13203000	0.84[EUR][1000 genomes]
rs13205013	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13206849	0.98[EUR][1000 genomes]
rs13210876	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13213878	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13217390	0.84[EUR][1000 genomes]
rs13219546	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13219942	0.86[EUR][1000 genomes]
rs16888085	0.90[ASN][1000 genomes]
rs16888096	1.00[ASN][1000 genomes]
rs16888106	1.00[ASN][1000 genomes]
rs16888118	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888124	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888126	0.95[EUR][1000 genomes]
rs16888128	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888135	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17684511	0.98[EUR][1000 genomes]
rs17684553	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17684571	1.00[EUR][1000 genomes]
rs17751682	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs17751695	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2144407	1.00[ASN][1000 genomes]
rs2180148	1.00[ASN][1000 genomes]
rs2967960	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2967963	0.83[EUR][1000 genomes]
rs3002003	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3002004	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3002006	0.84[EUR][1000 genomes]
rs3002007	0.83[EUR][1000 genomes]
rs3002008	0.84[EUR][1000 genomes]
rs3002009	0.84[EUR][1000 genomes]
rs3002010	0.84[EUR][1000 genomes]
rs3002011	0.84[EUR][1000 genomes]
rs34138864	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34429594	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34455199	0.84[EUR][1000 genomes]
rs34465210	0.84[EUR][1000 genomes]
rs34566275	0.84[EUR][1000 genomes]
rs34576803	0.97[EUR][1000 genomes]
rs34587484	0.84[EUR][1000 genomes]
rs34623351	0.84[EUR][1000 genomes]
rs34724718	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34803237	0.84[EUR][1000 genomes]
rs34812826	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34824960	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34832779	0.83[EUR][1000 genomes]
rs35089136	0.89[ASN][1000 genomes]
rs35206656	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35326806	0.86[EUR][1000 genomes]
rs35408048	0.98[EUR][1000 genomes]
rs35494794	0.86[EUR][1000 genomes]
rs35619924	0.98[EUR][1000 genomes]
rs35637749	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35668437	0.98[EUR][1000 genomes]
rs35687635	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35876418	0.84[EUR][1000 genomes]
rs35920751	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36068365	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4072271	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4073960	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4074101	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs4074102	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs4074103	0.94[CEU][hapmap];0.95[EUR][1000 genomes]
rs41267673	1.00[ASN][1000 genomes]
rs41267675	0.84[EUR][1000 genomes]
rs4133076	1.00[ASN][1000 genomes]
rs4262190	0.92[EUR][1000 genomes]
rs4275049	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4574644	0.89[ASN][1000 genomes]
rs4640889	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5024547	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs55742092	0.98[EUR][1000 genomes]
rs56094263	0.89[ASN][1000 genomes]
rs56101897	0.98[EUR][1000 genomes]
rs56196625	1.00[ASN][1000 genomes]
rs57289287	1.00[ASN][1000 genomes]
rs57392123	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs57488435	1.00[ASN][1000 genomes]
rs58565063	1.00[ASN][1000 genomes]
rs59073430	0.87[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs59085778	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59162324	0.89[ASN][1000 genomes]
rs59247267	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59772940	1.00[ASN][1000 genomes]
rs59889120	1.00[ASN][1000 genomes]
rs60360551	1.00[ASN][1000 genomes]
rs60498201	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62412526	0.98[EUR][1000 genomes]
rs62412528	0.98[EUR][1000 genomes]
rs62412531	0.98[EUR][1000 genomes]
rs62412532	0.98[EUR][1000 genomes]
rs62412556	0.84[EUR][1000 genomes]
rs6459167	1.00[ASN][1000 genomes]
rs6459168	1.00[ASN][1000 genomes]
rs6900572	1.00[ASN][1000 genomes]
rs6901176	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6903815	1.00[ASN][1000 genomes]
rs6916813	1.00[ASN][1000 genomes]
rs6924375	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6926134	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6938003	0.83[EUR][1000 genomes]
rs71564848	0.97[EUR][1000 genomes]
rs71564849	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73746926	1.00[ASN][1000 genomes]
rs73746929	1.00[ASN][1000 genomes]
rs73746930	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73746931	1.00[ASN][1000 genomes]
rs7749100	1.00[ASN][1000 genomes]
rs7749437	1.00[ASN][1000 genomes]
rs7759479	1.00[ASN][1000 genomes]
rs7760503	1.00[ASN][1000 genomes]
rs7760515	0.84[YRI][hapmap]
rs7760542	1.00[ASN][1000 genomes]
rs7761027	1.00[ASN][1000 genomes]
rs7767128	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56549800-56578000	Weak transcription	Gastric	stomach
2	chr6:56554000-56574600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr6:56555400-56574600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr6:56556200-56574400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:56558200-56578200	Weak transcription	Aorta	Aorta
6	chr6:56558400-56577800	Weak transcription	Ovary	ovary
7	chr6:56558400-56579400	Weak transcription	Right Ventricle	heart
8	chr6:56558600-56577800	Weak transcription	Fetal Heart	heart
9	chr6:56559800-56577800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr6:56560200-56579800	Weak transcription	Fetal Muscle Leg	muscle
11	chr6:56560400-56577200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:56562600-56574400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:56563000-56578000	Weak transcription	Psoas Muscle	Psoas
14	chr6:56564000-56577800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr6:56565000-56578000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:56565200-56574600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr6:56565400-56574200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:56568000-56580400	Weak transcription	Brain Germinal Matrix	brain
19	chr6:56568600-56577800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr6:56568800-56574400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr6:56570000-56574600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:56570000-56585600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr6:56570200-56574600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr6:56570200-56577800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr6:56570200-56590000	Weak transcription	Right Atrium	heart
26	chr6:56571400-56575200	Enhancers	Brain Cingulate Gyrus	brain
27	chr6:56571400-56575200	Enhancers	Brain Hippocampus Middle	brain
28	chr6:56571600-56576400	Enhancers	Brain Anterior Caudate	brain
29	chr6:56571800-56574200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr6:56571800-56575200	Enhancers	Brain Angular Gyrus	brain
31	chr6:56571800-56575200	Enhancers	Brain Substantia Nigra	brain
32	chr6:56572000-56578000	Weak transcription	Left Ventricle	heart
33	chr6:56572400-56574400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr6:56572400-56579400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr6:56572600-56574200	Enhancers	Hela-S3	cervix
36	chr6:56572600-56574600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr6:56572800-56575200	Enhancers	Rectal Smooth Muscle	rectum
38	chr6:56573000-56574400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr6:56573000-56574800	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr6:56573000-56577800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr6:56573200-56575200	Enhancers	Liver	Liver
42	chr6:56573200-56575200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr6:56573400-56574200	Enhancers	Stomach Mucosa	stomach
44	chr6:56573400-56574200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr6:56573400-56575000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr6:56573400-56575000	Enhancers	GM12878-XiMat	blood
47	chr6:56573400-56577600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr6:56573600-56574200	Active TSS	Osteobl	bone
49	chr6:56573600-56575200	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr6:56573600-56575400	Enhancers	HUES48 Cell Line	embryonic stem cell

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