Variant report

Variant	rs11084828
Chromosome Location	chr19:36213461-36213462
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:36207379..36214815-chr19:36234227..36241330,25	MCF-7	breast:

Variant related genes	Relation type
ENSG00000205155	Chromatin interaction
ENSG00000267796	Chromatin interaction
ENSG00000188223	Chromatin interaction
ENSG00000267439	Chromatin interaction
ENSG00000161265	Chromatin interaction
ENSG00000267120	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs107878	0.86[CEU][hapmap];0.89[GIH][hapmap];0.89[LWK][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs11667696	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11670414	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11671520	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11672164	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12151356	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12609803	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17776911	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.85[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2293687	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3746278	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3787051	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3848663	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.85[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3885794	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3885795	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4806197	0.87[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4806198	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4806201	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4806202	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs58561864	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66747537	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv911630	chr19:36149761-36290977	Enhancers Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	69 gene(s)	inside rSNPs	diseases
3	nsv458566	chr19:36156588-36265508	Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv579422	chr19:36156588-36265508	Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
5	nsv911631	chr19:36169285-36290977	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv911632	chr19:36174176-36288297	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv911633	chr19:36206050-36283847	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
8	nsv911634	chr19:36206050-36290977	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
9	nsv543996	chr19:36210269-36265431	Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
10	nsv1057830	chr19:36210269-36279794	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
11	nsv543997	chr19:36210269-36279794	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11084828	DEDD2	cis	cerebellum	SCAN
rs11084828	CEACAM4	cis	cerebellum	SCAN
rs11084828	LYPD3	cis	parietal	SCAN
rs11084828	ZFP36	cis	cerebellum	SCAN
rs11084828	FBXO17	cis	cerebellum	SCAN
rs11084828	NFKBIB	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36210400-36213800	Genic enhancers	Stomach Smooth Muscle	stomach
2	chr19:36210400-36215400	Weak transcription	Psoas Muscle	Psoas
3	chr19:36210400-36215600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr19:36210600-36213600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr19:36210600-36213600	Weak transcription	Fetal Kidney	kidney
6	chr19:36210600-36214200	Weak transcription	NH-A	brain
7	chr19:36210600-36215400	Weak transcription	NHDF-Ad	bronchial
8	chr19:36210600-36222400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr19:36210600-36223000	Strong transcription	Fetal Lung	lung
10	chr19:36210600-36223000	Strong transcription	Rectal Smooth Muscle	rectum
11	chr19:36210600-36223400	Strong transcription	Primary T cells from cord blood	blood
12	chr19:36210600-36230000	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr19:36210600-36230200	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr19:36210600-36230200	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr19:36210600-36230200	Strong transcription	Ovary	ovary
16	chr19:36210600-36230200	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr19:36210600-36230400	Strong transcription	Brain Inferior Temporal Lobe	brain
18	chr19:36210600-36230400	Strong transcription	A549	lung
19	chr19:36210600-36230600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr19:36210600-36230600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr19:36210600-36230600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr19:36210600-36230600	Weak transcription	Right Atrium	heart
23	chr19:36210600-36230600	Strong transcription	NHLF	lung
24	chr19:36210600-36231200	Weak transcription	Fetal Brain Male	brain
25	chr19:36210800-36214200	Genic enhancers	Primary T cells fromperipheralblood	blood
26	chr19:36210800-36215600	Weak transcription	Stomach Mucosa	stomach
27	chr19:36210800-36218600	Strong transcription	Brain Hippocampus Middle	brain
28	chr19:36210800-36221800	Strong transcription	NHEK	skin
29	chr19:36210800-36223600	Strong transcription	Colon Smooth Muscle	Colon
30	chr19:36210800-36225000	Strong transcription	Fetal Muscle Trunk	muscle
31	chr19:36210800-36227400	Strong transcription	Primary B cells from peripheral blood	blood
32	chr19:36210800-36228000	Strong transcription	Fetal Thymus	thymus
33	chr19:36210800-36229600	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr19:36210800-36229800	Strong transcription	Adipose Nuclei	Adipose
35	chr19:36210800-36230000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr19:36210800-36230200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr19:36210800-36230200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr19:36210800-36230200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr19:36210800-36230200	Strong transcription	Fetal Intestine Large	intestine
40	chr19:36210800-36230200	Strong transcription	Gastric	stomach
41	chr19:36210800-36230200	Strong transcription	Thymus	Thymus
42	chr19:36210800-36230400	Strong transcription	H9 Cell Line	embryonic stem cell
43	chr19:36210800-36230400	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr19:36210800-36230400	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr19:36210800-36230400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr19:36210800-36230400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr19:36210800-36230400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr19:36210800-36230400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr19:36210800-36230400	Strong transcription	Brain Cingulate Gyrus	brain
50	chr19:36210800-36230400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain

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