Variant report

Variant	rs11084156
Chromosome Location	chr19:52886887-52886888
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	chr19:52881938..52883510-chr19:52886057..52888201,2	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10445583	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10445584	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10445585	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1054612	0.95[CEU][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs11084150	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11084151	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11084152	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11084153	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11084154	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11084155	0.92[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11084157	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1993530	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1993531	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2042913	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2059817	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2059818	1.00[CEU][hapmap];0.87[CHB][hapmap];0.98[GIH][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2062971	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3170100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs324126	0.88[CEU][hapmap];0.87[TSI][hapmap]
rs34221182	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4802926	0.93[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[GIH][hapmap];0.97[LWK][hapmap];0.86[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55748277	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56151179	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60935857	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62108317	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62108318	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62108319	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62108320	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62108321	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8104808	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8104812	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv833873	chr19:52788939-52937281	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	esv3401193	chr19:52818960-52909749	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv912300	chr19:52832830-52928039	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv912301	chr19:52835210-52914233	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv912302	chr19:52859828-52928039	Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv2536	chr19:52869457-52902064	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv912303	chr19:52874140-52928039	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	esv3372061	chr19:52877189-52902218	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv521079	chr19:52886137-52917626	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11084156	ZNF880	trans	parietal	SCAN
rs11084156	ZNF880	cis	Nerve Tibial	GTEx
rs11084156	ZNF880	cis	Esophagus Muscularis	GTEx
rs11084156	LOC284379	cis	cerebellum	SCAN
rs11084156	LAIR2	cis	cerebellum	SCAN
rs11084156	LOC400713	Cis_1M	lymphoblastoid	RTeQTL
rs11084156	ZNF880	cis	Artery Tibial	GTEx
rs11084156	MZF1	cis	cerebellum	SCAN
rs11084156	ZNF880	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52873600-52888400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
2	chr19:52874000-52887200	ZNF genes & repeats	Fetal Intestine Large	intestine
3	chr19:52875600-52888600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
4	chr19:52876200-52888400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
5	chr19:52876200-52888800	ZNF genes & repeats	Primary T cells from cord blood	blood
6	chr19:52876200-52889000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
7	chr19:52876200-52889000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
8	chr19:52876200-52889000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
9	chr19:52876200-52889600	ZNF genes & repeats	Fetal Kidney	kidney
10	chr19:52876200-52889800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr19:52876200-52889800	ZNF genes & repeats	Fetal Brain Female	brain
12	chr19:52876200-52890000	ZNF genes & repeats	Ovary	ovary
13	chr19:52876200-52890600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr19:52876200-52890600	ZNF genes & repeats	Fetal Lung	lung
15	chr19:52876200-52890800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr19:52876200-52890800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
17	chr19:52876200-52890800	ZNF genes & repeats	Liver	Liver
18	chr19:52876200-52893400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
19	chr19:52876200-52893800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr19:52876200-52894000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr19:52876200-52894000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr19:52876200-52894200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:52876200-52895000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
24	chr19:52876400-52888000	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
25	chr19:52876400-52890600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
26	chr19:52876400-52891000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr19:52877400-52893800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
28	chr19:52877800-52889800	ZNF genes & repeats	Fetal Muscle Leg	muscle
29	chr19:52877800-52894200	ZNF genes & repeats	Adipose Nuclei	Adipose
30	chr19:52879000-52888800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
31	chr19:52879000-52889000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr19:52879000-52889800	ZNF genes & repeats	Primary B cells from cord blood	blood
33	chr19:52879000-52889800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr19:52879000-52890600	ZNF genes & repeats	Colon Smooth Muscle	Colon
35	chr19:52879600-52890400	ZNF genes & repeats	Brain Germinal Matrix	brain
36	chr19:52880200-52889000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr19:52880200-52889200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
38	chr19:52880200-52890600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr19:52880400-52893800	ZNF genes & repeats	Fetal Muscle Trunk	muscle
40	chr19:52882000-52890600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
41	chr19:52882600-52889000	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
42	chr19:52882800-52889200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr19:52883400-52889000	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
44	chr19:52883600-52887000	Strong transcription	Fetal Brain Male	brain
45	chr19:52884000-52889000	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
46	chr19:52884400-52887000	Weak transcription	Fetal Thymus	thymus
47	chr19:52884600-52889000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
48	chr19:52884600-52889000	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
49	chr19:52884600-52889800	ZNF genes & repeats	Dnd41	blood
50	chr19:52885000-52887800	ZNF genes & repeats	GM12878-XiMat	blood

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