Variant report

Variant	rs16888186
Chromosome Location	chr6:56731704-56731705
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56726286..56729119-chr6:56729880..56733046,4	MCF-7	breast:

Extended variants
information (count: 134 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs10498812	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs10498813	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs11970648	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs13190784	0.86[CEU][hapmap];1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs13190854	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13191826	1.00[ASN][1000 genomes]
rs13192540	0.93[EUR][1000 genomes]
rs13192931	0.93[EUR][1000 genomes]
rs13194625	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs13194904	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs13195601	0.90[EUR][1000 genomes]
rs13198204	0.83[EUR][1000 genomes]
rs13198597	0.93[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13200166	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs13200768	0.82[EUR][1000 genomes]
rs13200868	1.00[ASN][1000 genomes]
rs13201639	0.83[EUR][1000 genomes]
rs13201733	0.83[EUR][1000 genomes]
rs13203148	0.89[EUR][1000 genomes]
rs13203681	0.88[CEU][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13204466	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs13205667	0.88[CEU][hapmap]
rs13207768	0.87[CEU][hapmap];0.95[EUR][1000 genomes]
rs13209099	0.86[CEU][hapmap]
rs13211879	0.88[EUR][1000 genomes]
rs13214893	0.99[EUR][1000 genomes]
rs13215883	0.93[CEU][hapmap];0.98[EUR][1000 genomes]
rs13218913	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs13220618	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs13220628	0.86[CEU][hapmap];0.89[EUR][1000 genomes]
rs13220851	0.84[EUR][1000 genomes]
rs1610156	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1610157	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16888171	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs16888184	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16888189	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs16888192	0.86[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17684730	0.83[EUR][1000 genomes]
rs17684748	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs17684772	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs17684784	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs17684802	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs17684878	0.87[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17684884	0.88[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17684941	0.98[EUR][1000 genomes]
rs17751966	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs17751977	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs17752002	0.83[EUR][1000 genomes]
rs17752046	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs17752106	0.87[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17752213	0.99[EUR][1000 genomes]
rs1870638	0.81[CEU][hapmap]
rs1903332	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28360570	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3002010	1.00[CHB][hapmap]
rs3002011	1.00[CHB][hapmap]
rs34083827	0.98[EUR][1000 genomes]
rs34171958	0.84[EUR][1000 genomes]
rs34228698	0.83[EUR][1000 genomes]
rs34359353	0.84[EUR][1000 genomes]
rs34425815	0.82[EUR][1000 genomes]
rs34520435	0.84[EUR][1000 genomes]
rs34612783	0.82[EUR][1000 genomes]
rs34614087	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34640766	0.83[EUR][1000 genomes]
rs34866877	0.90[EUR][1000 genomes]
rs34896026	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34966024	1.00[ASN][1000 genomes]
rs35073881	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35080938	0.94[EUR][1000 genomes]
rs35081015	0.89[EUR][1000 genomes]
rs35225175	0.89[EUR][1000 genomes]
rs35242294	0.95[EUR][1000 genomes]
rs35251663	0.82[EUR][1000 genomes]
rs35407078	0.90[EUR][1000 genomes]
rs35439100	0.90[EUR][1000 genomes]
rs35440408	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35440822	0.84[EUR][1000 genomes]
rs35461301	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35566812	0.81[EUR][1000 genomes]
rs35609883	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35642890	0.83[EUR][1000 genomes]
rs35696739	0.83[EUR][1000 genomes]
rs35828379	0.93[EUR][1000 genomes]
rs35851452	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35873865	0.81[EUR][1000 genomes]
rs35886823	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36022925	0.83[EUR][1000 genomes]
rs36037734	0.83[EUR][1000 genomes]
rs36094082	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4299824	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs4348308	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs4371846	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs4415160	0.87[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4457154	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs4532444	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4587171	0.85[YRI][hapmap];0.80[EUR][1000 genomes]
rs56037312	0.80[EUR][1000 genomes]
rs58980183	1.00[ASN][1000 genomes]
rs59432342	0.83[EUR][1000 genomes]
rs60163288	1.00[ASN][1000 genomes]
rs61601344	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62411372	0.82[EUR][1000 genomes]
rs62411375	0.82[EUR][1000 genomes]
rs62411376	0.83[EUR][1000 genomes]
rs6904535	1.00[ASN][1000 genomes]
rs6905603	0.88[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6905658	0.87[ASN][1000 genomes]
rs6910414	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914293	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6918949	0.87[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6925518	0.87[ASN][1000 genomes]
rs6926742	0.87[ASN][1000 genomes]
rs6934714	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71564854	0.83[EUR][1000 genomes]
rs71564855	0.84[EUR][1000 genomes]
rs71564856	0.83[EUR][1000 genomes]
rs71564861	0.83[EUR][1000 genomes]
rs71564863	0.93[EUR][1000 genomes]
rs7744240	0.80[CEU][hapmap]
rs7744799	0.86[CEU][hapmap]
rs7758867	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7761501	0.87[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7761729	0.87[CEU][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7766565	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7771085	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs7775182	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
6	nsv1022714	chr6:56729767-56826642	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv538229	chr6:56729767-56826642	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16888186	RP11-472M19.2	cis	Heart Left Ventricle	GTEx

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56723000-56732600	Weak transcription	Small Intestine	intestine
2	chr6:56724200-56733800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr6:56725600-56734800	Enhancers	Hela-S3	cervix
4	chr6:56727200-56734600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:56727600-56734400	Enhancers	HMEC	breast
6	chr6:56727800-56734800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr6:56728000-56731800	Weak transcription	Spleen	Spleen
8	chr6:56728000-56734800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:56728000-56735000	Enhancers	HSMM	muscle
10	chr6:56728000-56735000	Enhancers	NHDF-Ad	bronchial
11	chr6:56728200-56733800	Enhancers	HSMMtube	muscle
12	chr6:56728200-56733800	Enhancers	Osteobl	bone
13	chr6:56728800-56734800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:56729000-56733000	Enhancers	Muscle Satellite Cultured Cells	--
15	chr6:56729200-56731800	Weak transcription	GM12878-XiMat	blood
16	chr6:56729200-56733000	Enhancers	A549	lung
17	chr6:56729400-56731800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:56729400-56731800	Weak transcription	NH-A	brain
19	chr6:56729600-56732200	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr6:56730000-56732000	Enhancers	H1 Cell Line	embryonic stem cell
21	chr6:56730000-56732000	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr6:56730000-56732200	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr6:56730000-56733000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr6:56730200-56732000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr6:56730400-56731800	Weak transcription	Fetal Intestine Large	intestine
26	chr6:56730400-56731800	Weak transcription	Fetal Intestine Small	intestine
27	chr6:56730400-56732200	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr6:56730400-56733800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr6:56730400-56740400	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr6:56730600-56733000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:56730600-56733000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr6:56730600-56733000	Weak transcription	NHEK	skin
33	chr6:56730800-56733000	Enhancers	HUVEC	blood vessel
34	chr6:56731000-56732200	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr6:56731000-56732400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr6:56731000-56732600	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr6:56731000-56733200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr6:56731200-56731800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr6:56731200-56732000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr6:56731200-56732400	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr6:56731400-56732000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr6:56731600-56731800	Enhancers	NHLF	lung
43	chr6:56731600-56732600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr6:56731600-56733000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr6:56731600-56734600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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