Variant report

Variant	rs882520
Chromosome Location	chr19:42389280-42389281
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:42389226..42390893-chr19:42441627..42443907,2	MCF-7	breast:
2	chr19:42385735..42391033-chr19:42460351..42463651,6	K562	blood:
3	chr19:42386056..42389793-chr19:42407267..42411147,5	MCF-7	breast:
4	chr19:42388132..42389933-chr19:42401964..42404218,2	K562	blood:
5	chr19:42385706..42396512-chr19:42423854..42433641,19	K562	blood:
6	chr19:42389117..42392218-chr19:42417443..42420229,3	K562	blood:
7	chr19:42385318..42391505-chr19:42458040..42463569,9	MCF-7	breast:
8	chr19:42382327..42390135-chr19:42429723..42437438,12	MCF-7	breast:
9	chr19:42387685..42389812-chr19:42806888..42808559,2	K562	blood:
10	chr19:42388358..42390538-chr19:42579521..42581745,2	MCF-7	breast:
11	chr19:42389117..42391614-chr19:42418078..42420063,2	K562	blood:
12	chr19:42384855..42393410-chr19:42428364..42439251,22	K562	blood:
13	chr19:42389271..42392129-chr19:42772552..42774561,2	MCF-7	breast:
14	chr19:42386109..42390387-chr19:42411996..42416642,6	K562	blood:
15	chr19:42385036..42390018-chr19:42460408..42463391,5	K562	blood:
16	chr19:42387951..42392334-chr19:42459610..42463737,7	MCF-7	breast:
17	chr19:42388986..42391635-chr2:199208235..199210709,2	MCF-7	breast:
18	chr19:42362804..42368897-chr19:42386582..42393421,16	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000268041	Chromatin interaction
ENSG00000079432	Chromatin interaction
ENSG00000105404	Chromatin interaction
ENSG00000105372	Chromatin interaction
ENSG00000105732	Chromatin interaction
ENSG00000079462	Chromatin interaction
ENSG00000076928	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10404939	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs10405900	0.99[ASN][1000 genomes]
rs10408367	0.82[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs10414823	0.91[CHB][hapmap]
rs10415452	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10416824	0.82[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs10417985	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10500284	0.82[CEU][hapmap];0.95[CHB][hapmap]
rs12461099	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12461131	0.87[ASN][1000 genomes]
rs12972552	0.80[EUR][1000 genomes]
rs12976571	0.96[CHB][hapmap];0.82[JPT][hapmap]
rs12979253	0.82[CEU][hapmap];0.91[CHB][hapmap]
rs12984383	0.81[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs1366610	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs1428922	0.99[ASN][1000 genomes]
rs1457144	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs1870092	0.82[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap]
rs2008798	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs2075749	0.86[ASN][1000 genomes]
rs2075750	0.81[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs2075752	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2075754	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs2199829	0.82[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs2290695	0.95[CHB][hapmap]
rs2305809	0.95[CHB][hapmap]
rs3786536	0.82[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs3786538	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs3810153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3922888	0.95[CHB][hapmap]
rs4803511	0.95[CHB][hapmap]
rs4803512	0.91[CHB][hapmap]
rs58857981	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6509002	0.87[CHB][hapmap]
rs7250787	0.87[ASN][1000 genomes]
rs7251336	0.82[CEU][hapmap]
rs7251960	0.82[CEU][hapmap]
rs7254214	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7257666	0.88[ASN][1000 genomes]
rs7258163	0.83[ASN][1000 genomes]
rs7259596	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7259967	0.96[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs734107	0.82[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap]
rs73549152	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs8102670	0.85[ASN][1000 genomes]
rs8104958	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs8106505	0.91[CHB][hapmap]
rs8113283	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs8113641	0.84[CHB][hapmap];0.82[JPT][hapmap];0.88[YRI][hapmap]
rs873282	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs891167	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs899662	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs930102	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv1061878	chr19:42325490-42416056	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv911776	chr19:42343526-42416056	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv911777	chr19:42357455-42521108	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
6	nsv911778	chr19:42358362-42416056	Strong transcription Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs882520	RABAC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42386800-42389400	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
2	chr19:42386800-42389400	Active TSS	Rectal Smooth Muscle	rectum
3	chr19:42387000-42389400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr19:42387000-42390200	Active TSS	Primary T cells from cord blood	blood
5	chr19:42387400-42389400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
6	chr19:42387600-42390400	Transcr. at gene 5' and 3'	Dnd41	blood
7	chr19:42387800-42389600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr19:42388000-42389400	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr19:42388400-42389600	Flanking Active TSS	Primary B cells from cord blood	blood
10	chr19:42388600-42389400	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
11	chr19:42388600-42389400	Flanking Active TSS	Primary hematopoietic stem cells	blood
12	chr19:42388600-42389400	Transcr. at gene 5' and 3'	Primary T helper naive cells from peripheral blood	blood
13	chr19:42388600-42389400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
14	chr19:42388600-42389400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr19:42388600-42389400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr19:42388600-42389400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr19:42388600-42389400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr19:42388600-42389400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
19	chr19:42388600-42389400	Flanking Active TSS	Brain Germinal Matrix	brain
20	chr19:42388600-42389400	Flanking Active TSS	Colonic Mucosa	Colon
21	chr19:42388600-42389400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
22	chr19:42388600-42389400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr19:42388600-42389400	Flanking Active TSS	Stomach Smooth Muscle	stomach
24	chr19:42388600-42391400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
25	chr19:42388800-42389400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr19:42388800-42389400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr19:42388800-42389400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr19:42388800-42389400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
29	chr19:42388800-42389400	Transcr. at gene 5' and 3'	Primary Natural Killer cells fromperipheralblood	blood
30	chr19:42388800-42389400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
31	chr19:42388800-42389400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
32	chr19:42388800-42389400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr19:42388800-42389400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
34	chr19:42388800-42389400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr19:42388800-42389400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr19:42388800-42389400	Flanking Active TSS	Brain Angular Gyrus	brain
37	chr19:42388800-42389400	Flanking Active TSS	Brain Anterior Caudate	brain
38	chr19:42388800-42389400	Flanking Active TSS	Brain Cingulate Gyrus	brain
39	chr19:42388800-42389400	Flanking Active TSS	Brain Hippocampus Middle	brain
40	chr19:42388800-42389400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
41	chr19:42388800-42389400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr19:42388800-42389400	Flanking Active TSS	Brain Substantia Nigra	brain
43	chr19:42388800-42389400	Flanking Active TSS	Colon Smooth Muscle	Colon
44	chr19:42388800-42389400	Flanking Active TSS	Duodenum Mucosa	Duodenum
45	chr19:42388800-42389400	Flanking Active TSS	Fetal Intestine Small	intestine
46	chr19:42388800-42389400	Flanking Active TSS	Fetal Stomach	stomach
47	chr19:42388800-42389400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
48	chr19:42388800-42389400	Flanking Active TSS	Sigmoid Colon	Sigmoid Colon
49	chr19:42388800-42389400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr19:42388800-42389400	Flanking Active TSS	Hela-S3	cervix

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