Variant report

Variant	rs1071880
Chromosome Location	chr11:34446221-34446222
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1033509	0.82[ASN][1000 genomes]
rs10742316	0.82[ASN][1000 genomes]
rs16925614	0.94[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2076556	1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs208675	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs208677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs208680	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs208681	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs208682	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs208683	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2300182	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2746169	0.82[ASN][1000 genomes]
rs4755374	0.94[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4756146	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs489554	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5026711	0.82[ASN][1000 genomes]
rs554518	0.88[EUR][1000 genomes]
rs564250	0.87[ASN][1000 genomes]
rs7102889	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs7109778	0.94[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs72923163	0.94[AFR][1000 genomes]
rs7395059	0.84[AFR][1000 genomes]
rs7938373	1.00[YRI][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	nsv897205	chr11:34248229-34507213	Enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv897207	chr11:34253683-34621004	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv897208	chr11:34257064-34562247	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv897209	chr11:34309519-34548906	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv832114	chr11:34424428-34607851	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1071880	CAT	cis	Whole Blood	GTEx
rs1071880	CAT	cis	multi-tissue	Pritchard
rs1071880	CAT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:34438200-34448600	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr11:34440200-34447000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr11:34440200-34447400	Weak transcription	Hela-S3	cervix
4	chr11:34443400-34450000	Enhancers	Primary hematopoietic stem cells	blood
5	chr11:34443800-34460000	Weak transcription	Esophagus	oesophagus
6	chr11:34444200-34447400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr11:34444200-34447400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr11:34444200-34447400	Weak transcription	A549	lung
9	chr11:34444200-34447400	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr11:34444200-34447400	Weak transcription	NHLF	lung
11	chr11:34444400-34447800	Weak transcription	Liver	Liver
12	chr11:34444600-34446600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr11:34445000-34447600	Weak transcription	K562	blood
14	chr11:34445000-34449400	Enhancers	HMEC	breast
15	chr11:34445200-34446800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr11:34445200-34446800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr11:34445200-34447800	Weak transcription	Primary B cells from cord blood	blood
18	chr11:34445400-34447400	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr11:34445400-34448200	Weak transcription	Fetal Lung	lung
20	chr11:34445400-34448600	Weak transcription	Lung	lung
21	chr11:34445600-34448200	Weak transcription	Placenta	Placenta
22	chr11:34445800-34447400	Weak transcription	Adipose Nuclei	Adipose
23	chr11:34446200-34446600	Weak transcription	Primary monocytes fromperipheralblood	blood

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