Variant report

Variant	rs11576878
Chromosome Location	chr1:161775577-161775578
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:161770427..161772901-chr1:161774047..161776323,2	MCF-7	breast:
2	chr1:161771151..161773620-chr1:161774847..161776927,2	MCF-7	breast:
3	chr1:161768961..161773508-chr1:161774562..161778205,4	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1006310	0.84[CHD][hapmap]
rs1027700	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1058405	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10918243	0.89[ASN][1000 genomes]
rs11579627	0.82[ASW][hapmap];0.85[CEU][hapmap];0.90[GIH][hapmap];0.85[MKK][hapmap]
rs11581556	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11590304	0.89[ASN][1000 genomes]
rs12130299	0.85[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs1847383	0.82[ASN][1000 genomes]
rs3767634	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3820449	0.85[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs4657106	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657121	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56041058	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs61801240	0.81[ASN][1000 genomes]
rs61802507	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7414603	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7519514	0.86[CHB][hapmap]
rs7529356	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs905594	0.86[CHB][hapmap];0.84[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428257	chr1:161406315-161868263	Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv33393	chr1:161478681-162080327	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv464184	chr1:161646807-161885352	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv548075	chr1:161646807-161885352	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11576878	CD1A	cis	parietal	SCAN
rs11576878	OTUD5	trans	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161737200-161775800	Weak transcription	Stomach Mucosa	stomach
2	chr1:161737200-161780000	Weak transcription	Fetal Intestine Small	intestine
3	chr1:161738600-161794000	Weak transcription	Pancreas	Pancrea
4	chr1:161738600-161795600	Weak transcription	Gastric	stomach
5	chr1:161745400-161780000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:161748000-161778800	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr1:161748200-161780000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr1:161749000-161777000	Strong transcription	Liver	Liver
9	chr1:161749200-161780000	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr1:161752200-161780000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:161752600-161776000	Weak transcription	Fetal Heart	heart
12	chr1:161753200-161780000	Weak transcription	Esophagus	oesophagus
13	chr1:161753400-161800600	Weak transcription	Spleen	Spleen
14	chr1:161755000-161793600	Weak transcription	Colonic Mucosa	Colon
15	chr1:161755400-161780000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:161756200-161776800	Strong transcription	Primary B cells from cord blood	blood
17	chr1:161757400-161778400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr1:161757400-161797000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:161759600-161777400	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr1:161760400-161780200	Weak transcription	A549	lung
21	chr1:161760800-161777200	Strong transcription	Primary B cells from peripheral blood	blood
22	chr1:161762200-161776000	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr1:161762200-161779800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr1:161762200-161780000	Weak transcription	Thymus	Thymus
25	chr1:161762200-161790600	Weak transcription	Fetal Brain Male	brain
26	chr1:161762400-161779800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr1:161762400-161790800	Weak transcription	NH-A	brain
28	chr1:161762400-161791200	Weak transcription	Right Ventricle	heart
29	chr1:161762400-161795400	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr1:161762800-161797600	Weak transcription	HMEC	breast
31	chr1:161763000-161797400	Weak transcription	NHLF	lung
32	chr1:161763400-161779800	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr1:161763400-161780000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr1:161764800-161780200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:161765800-161779800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr1:161765800-161779800	Weak transcription	Ovary	ovary
37	chr1:161765800-161780200	Weak transcription	Brain Angular Gyrus	brain
38	chr1:161766000-161776000	Weak transcription	Brain Hippocampus Middle	brain
39	chr1:161766000-161780600	Weak transcription	Brain Anterior Caudate	brain
40	chr1:161766000-161790800	Weak transcription	Lung	lung
41	chr1:161767400-161779800	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr1:161767400-161791200	Weak transcription	Aorta	Aorta
43	chr1:161767600-161776400	Weak transcription	Fetal Brain Female	brain
44	chr1:161767800-161775600	Weak transcription	Stomach Smooth Muscle	stomach
45	chr1:161768000-161779800	Weak transcription	Fetal Lung	lung
46	chr1:161768000-161780000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr1:161768000-161789400	Weak transcription	HepG2	liver
48	chr1:161769400-161776400	Weak transcription	Fetal Muscle Leg	muscle
49	chr1:161771400-161776800	Strong transcription	Placenta	Placenta
50	chr1:161772000-161779000	Weak transcription	Left Ventricle	heart

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