Variant report

Variant	rs541811
Chromosome Location	chr13:96672110-96672111
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:96672084..96672616-chr13:97469396..97470262,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1980942	0.91[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.87[EUR][1000 genomes]
rs1996054	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2389530	0.80[CEU][hapmap]
rs2389531	0.82[EUR][1000 genomes]
rs2774113	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2849438	0.85[EUR][1000 genomes]
rs3099358	0.86[CHB][hapmap]
rs3099359	0.90[ASW][hapmap];0.86[YRI][hapmap]
rs3099360	0.91[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.81[TSI][hapmap]
rs472788	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs473930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4773927	0.81[ASW][hapmap]
rs4773930	0.89[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.93[YRI][hapmap]
rs481927	0.82[EUR][1000 genomes]
rs489179	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs493109	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs506474	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs509572	0.88[CEU][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs511029	0.83[EUR][1000 genomes]
rs517173	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs521235	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs527680	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs529306	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs531090	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs532399	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs536606	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs537571	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs539604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs544080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs551457	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs552598	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs555221	0.82[EUR][1000 genomes]
rs561996	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs566894	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs576184	0.90[ASW][hapmap];0.88[CEU][hapmap];0.86[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs590758	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs592205	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs595696	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs6492826	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7333045	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.93[YRI][hapmap];0.82[EUR][1000 genomes]
rs7992824	0.83[EUR][1000 genomes]
rs7993804	0.81[EUR][1000 genomes]
rs7994626	0.86[YRI][hapmap]
rs7998903	0.86[YRI][hapmap]
rs816139	0.91[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.87[JPT][hapmap];0.82[LWK][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs816143	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9516620	0.93[YRI][hapmap]
rs9516626	0.89[EUR][1000 genomes]
rs9516629	0.81[AFR][1000 genomes]
rs9525081	0.86[EUR][1000 genomes]
rs9525085	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.85[EUR][1000 genomes]
rs9525086	0.87[EUR][1000 genomes]
rs9525093	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9525095	0.91[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap]
rs9525098	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9561979	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9742440	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050430	chr13:96508530-97020734	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv541883	chr13:96508530-97020734	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1041165	chr13:96522021-96966520	Enhancers Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1051574	chr13:96550653-96779248	Strong transcription Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1040320	chr13:96573646-96790859	Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv869471	chr13:96622327-97223956	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs541811	DZIP1	cis	cerebellum	SCAN
rs541811	DZIP1	cis	parietal	SCAN
rs541811	UGCGL2	cis	multi-tissue	Pritchard

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96613200-96694200	Weak transcription	A549	lung
2	chr13:96622200-96677200	Weak transcription	NH-A	brain
3	chr13:96657800-96677200	Weak transcription	HSMMtube	muscle
4	chr13:96659400-96672600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr13:96660200-96682200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr13:96660400-96678600	Weak transcription	Duodenum Mucosa	Duodenum
7	chr13:96660600-96676600	Weak transcription	Osteobl	bone
8	chr13:96660800-96672600	Weak transcription	Liver	Liver
9	chr13:96660800-96684800	Weak transcription	Psoas Muscle	Psoas
10	chr13:96663200-96685400	Weak transcription	HMEC	breast
11	chr13:96663800-96672600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr13:96664000-96677200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr13:96664200-96677600	Weak transcription	NHDF-Ad	bronchial
14	chr13:96664200-96684800	Weak transcription	NHLF	lung
15	chr13:96667200-96672200	Weak transcription	Brain Hippocampus Middle	brain
16	chr13:96668400-96672600	Weak transcription	Brain Substantia Nigra	brain
17	chr13:96668600-96679400	Weak transcription	Fetal Brain Male	brain
18	chr13:96668600-96704400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr13:96668800-96672800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr13:96668800-96673600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr13:96668800-96685400	Weak transcription	Gastric	stomach
22	chr13:96669000-96683200	Weak transcription	Esophagus	oesophagus
23	chr13:96669000-96685800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr13:96669000-96686200	Weak transcription	NHEK	skin
25	chr13:96669200-96672400	Strong transcription	Fetal Stomach	stomach
26	chr13:96669200-96686800	Weak transcription	Right Ventricle	heart
27	chr13:96669200-96694000	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr13:96669400-96672200	Weak transcription	GM12878-XiMat	blood
29	chr13:96669400-96672600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr13:96669400-96672600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr13:96669400-96673000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr13:96669400-96676600	Weak transcription	Aorta	Aorta
33	chr13:96669400-96677000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr13:96669400-96677000	Weak transcription	Brain Germinal Matrix	brain
35	chr13:96669400-96677200	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr13:96669400-96677200	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr13:96669400-96680000	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr13:96669400-96685400	Weak transcription	Fetal Kidney	kidney
39	chr13:96669400-96685600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr13:96669400-96685600	Weak transcription	Fetal Brain Female	brain
41	chr13:96669400-96694000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr13:96669400-96704600	Weak transcription	Brain Anterior Caudate	brain
43	chr13:96669600-96672200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr13:96669600-96674200	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr13:96669600-96677400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr13:96669600-96686400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr13:96669600-96686400	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr13:96669600-96687000	Weak transcription	Adipose Nuclei	Adipose
49	chr13:96669800-96672200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr13:96669800-96672200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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