Variant report

Variant	rs4072271
Chromosome Location	chr6:56572477-56572478
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	chr6:56572377..56575419-chr6:56576421..56579962,3	MCF-7	breast:

Extended variants
information (count: 144 )
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	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11961342	0.82[AMR][1000 genomes];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];0.84[AMR][1000 genomes];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	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13192037	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs13192478	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13192567	0.82[AMR][1000 genomes];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	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13206849	0.98[EUR][1000 genomes]
rs13210876	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13213878	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13217390	0.84[EUR][1000 genomes]
rs13219546	0.84[AMR][1000 genomes];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	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888124	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888126	0.95[EUR][1000 genomes]
rs16888128	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888130	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888133	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888135	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16888171	1.00[CHD][hapmap];0.81[MEX][hapmap]
rs17684511	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];0.98[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	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2967963	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3002003	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3002004	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3002006	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3002007	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3002008	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3002009	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3002010	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3002011	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34138864	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34429594	0.80[AMR][1000 genomes];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	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34803237	0.84[EUR][1000 genomes]
rs34812826	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34824960	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34832779	0.83[EUR][1000 genomes]
rs35089136	0.89[ASN][1000 genomes]
rs35206656	0.91[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	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35668437	0.98[EUR][1000 genomes]
rs35687635	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35876418	0.84[EUR][1000 genomes]
rs35920751	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36068365	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4073960	0.89[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];0.98[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[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4574644	0.89[ASN][1000 genomes]
rs4640889	0.84[AMR][1000 genomes];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	1.00[ASN][1000 genomes]
rs57488435	1.00[ASN][1000 genomes]
rs58565063	1.00[ASN][1000 genomes]
rs59073430	1.00[ASN][1000 genomes]
rs59085778	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59162324	0.89[ASN][1000 genomes]
rs59247267	0.84[AMR][1000 genomes];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	0.80[AMR][1000 genomes];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	0.88[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];0.90[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6926134	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6938003	0.82[AMR][1000 genomes];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	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];0.86[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7775134	1.00[CHD][hapmap]

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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4072271	LRRC1	cis	cerebellum	SCAN
rs4072271	BMP5	cis	cerebellum	SCAN
rs4072271	DST	cis	cerebellum	SCAN

Chromatin state (count:68 , 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	chr6:56558200-56573400	Weak transcription	Stomach Mucosa	stomach
9	chr6:56558200-56578200	Weak transcription	Aorta	Aorta
10	chr6:56558400-56573200	Weak transcription	Adipose Nuclei	Adipose
11	chr6:56558400-56577800	Weak transcription	Ovary	ovary
12	chr6:56558400-56579400	Weak transcription	Right Ventricle	heart
13	chr6:56558600-56577800	Weak transcription	Fetal Heart	heart
14	chr6:56559600-56572600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr6:56559600-56573000	Weak transcription	NH-A	brain
16	chr6:56559800-56577800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr6:56560200-56579800	Weak transcription	Fetal Muscle Leg	muscle
18	chr6:56560400-56577200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:56561400-56573200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr6:56562000-56573200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr6:56562600-56574400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr6:56563000-56578000	Weak transcription	Psoas Muscle	Psoas
23	chr6:56563600-56573400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:56564000-56573200	Weak transcription	Liver	Liver
25	chr6:56564000-56577800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr6:56565000-56578000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr6:56565200-56572800	Weak transcription	GM12878-XiMat	blood
28	chr6:56565200-56574600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr6:56565400-56574200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:56568000-56580400	Weak transcription	Brain Germinal Matrix	brain
31	chr6:56568600-56573400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr6:56568600-56577800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr6:56568800-56572800	Weak transcription	HUVEC	blood vessel
34	chr6:56568800-56574400	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr6:56570000-56574600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr6:56570000-56585600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr6:56570200-56573400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr6:56570200-56573400	Weak transcription	A549	lung
39	chr6:56570200-56574600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr6:56570200-56577800	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr6:56570200-56590000	Weak transcription	Right Atrium	heart
42	chr6:56571400-56573800	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr6:56571400-56575200	Enhancers	Brain Cingulate Gyrus	brain
44	chr6:56571400-56575200	Enhancers	Brain Hippocampus Middle	brain
45	chr6:56571600-56576400	Enhancers	Brain Anterior Caudate	brain
46	chr6:56571800-56572600	Enhancers	Colon Smooth Muscle	Colon
47	chr6:56571800-56572800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr6:56571800-56573200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr6:56571800-56573800	Enhancers	HSMMtube	muscle
50	chr6:56571800-56574000	Enhancers	Skeletal Muscle Male	skeletal muscle

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