Variant report

Variant	rs16888128
Chromosome Location	chr6:56569104-56569105
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:56567530..56570297-chr6:56577353..56579502,2	MCF-7	breast:

Extended variants
information (count: 142 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:139)

rs_ID	r²[population]
rs1024196	1.00[CHD][hapmap];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	1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11970410	0.90[ASN][1000 genomes]
rs11970648	1.00[CHD][hapmap];1.00[MEX][hapmap]
rs13190784	1.00[CHD][hapmap];0.81[MEX][hapmap]
rs13191164	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13192037	1.00[CEU][hapmap];0.81[AMR][1000 genomes];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	0.91[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	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888124	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888126	0.95[EUR][1000 genomes]
rs16888130	1.00[CEU][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888133	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888135	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16888171	1.00[CHD][hapmap];0.81[MEX][hapmap]
rs17684511	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17684553	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17684571	1.00[EUR][1000 genomes]
rs17684878	0.81[MEX][hapmap]
rs17751682	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs17751695	1.00[CEU][hapmap];0.87[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1903332	1.00[CHD][hapmap];0.81[MEX][hapmap]
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	0.89[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	0.90[AFR][1000 genomes];0.98[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	1.00[AFR][1000 genomes];0.92[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	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35668437	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35687635	1.00[AFR][1000 genomes];0.92[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	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4073960	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4074101	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4074102	1.00[CEU][hapmap];0.81[AMR][1000 genomes];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	0.80[AMR][1000 genomes];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	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56196625	1.00[ASN][1000 genomes]
rs57289287	1.00[ASN][1000 genomes]
rs57392123	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs57488435	1.00[ASN][1000 genomes]
rs58565063	1.00[ASN][1000 genomes]
rs59073430	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	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62412531	0.81[AMR][1000 genomes];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	0.89[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]
rs6918949	0.81[MEX][hapmap]
rs6924375	1.00[CEU][hapmap];0.93[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	1.00[EUR][1000 genomes]
rs73746926	1.00[ASN][1000 genomes]
rs73746929	1.00[ASN][1000 genomes]
rs73746930	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73746931	1.00[ASN][1000 genomes]
rs7749100	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs7749437	1.00[ASN][1000 genomes]
rs7758867	1.00[CHD][hapmap];0.81[MEX][hapmap]
rs7759479	1.00[ASN][1000 genomes]
rs7760503	1.00[ASN][1000 genomes]
rs7760542	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs7761027	1.00[ASN][1000 genomes]
rs7761729	0.81[MEX][hapmap]
rs7767128	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7775134	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16888128	BMP5	cis	cerebellum	SCAN
rs16888128	LRRC1	cis	cerebellum	SCAN
rs16888128	DST	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56549600-56573600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr6:56549800-56578000	Weak transcription	Gastric	stomach
3	chr6:56554000-56574600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr6:56555400-56574600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr6:56555800-56573600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr6:56556200-56573600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr6:56556200-56574400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:56558200-56569800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:56558200-56573400	Weak transcription	Stomach Mucosa	stomach
10	chr6:56558200-56578200	Weak transcription	Aorta	Aorta
11	chr6:56558400-56571600	Weak transcription	Fetal Stomach	stomach
12	chr6:56558400-56573200	Weak transcription	Adipose Nuclei	Adipose
13	chr6:56558400-56577800	Weak transcription	Ovary	ovary
14	chr6:56558400-56579400	Weak transcription	Right Ventricle	heart
15	chr6:56558600-56577800	Weak transcription	Fetal Heart	heart
16	chr6:56559600-56572600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:56559600-56573000	Weak transcription	NH-A	brain
18	chr6:56559800-56577800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:56560200-56579800	Weak transcription	Fetal Muscle Leg	muscle
20	chr6:56560400-56569800	Weak transcription	Brain Anterior Caudate	brain
21	chr6:56560400-56577200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr6:56560600-56572200	Weak transcription	NHDF-Ad	bronchial
23	chr6:56560600-56572400	Weak transcription	HMEC	breast
24	chr6:56561200-56571800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr6:56561400-56573200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr6:56562000-56569800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:56562000-56569800	Weak transcription	Left Ventricle	heart
28	chr6:56562000-56573200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr6:56562200-56571600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr6:56562400-56569800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr6:56562600-56572400	Weak transcription	NHLF	lung
32	chr6:56562600-56574400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr6:56562800-56569800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr6:56563000-56569800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr6:56563000-56571800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr6:56563000-56578000	Weak transcription	Psoas Muscle	Psoas
37	chr6:56563600-56573400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr6:56563800-56569400	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr6:56564000-56569800	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr6:56564000-56573200	Weak transcription	Liver	Liver
41	chr6:56564000-56577800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr6:56565000-56578000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr6:56565200-56572800	Weak transcription	GM12878-XiMat	blood
44	chr6:56565200-56574600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr6:56565400-56574200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:56566400-56571600	Strong transcription	HSMM	muscle
47	chr6:56567400-56569800	Weak transcription	A549	lung
48	chr6:56567800-56569800	Weak transcription	Brain Hippocampus Middle	brain
49	chr6:56567800-56570200	Enhancers	Brain Angular Gyrus	brain
50	chr6:56567800-56571400	Weak transcription	Rectal Smooth Muscle	rectum

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