Variant report

Variant	rs7259596
Chromosome Location	chr19:42369743-42369744
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:42354940..42358615-chr19:42368975..42372693,4	K562	blood:
2	chr19:42354721..42357873-chr19:42369180..42372292,3	MCF-7	breast:
3	chr19:42369015..42372839-chr19:42460520..42463128,4	K562	blood:
4	chr19:42346920..42348959-chr19:42369071..42372047,3	K562	blood:
5	chr19:42368937..42370473-chr19:42375983..42377700,2	MCF-7	breast:
6	chr19:42369679..42372709-chr19:42429800..42433926,4	K562	blood:

Variant related genes	Relation type
ENSG00000076928	Chromatin interaction
ENSG00000142025	Chromatin interaction
ENSG00000105404	Chromatin interaction
ENSG00000183103	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10404939	0.82[ASN][1000 genomes]
rs10405900	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10414356	0.83[ASN][1000 genomes]
rs10415452	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10417985	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10500284	0.84[ASN][1000 genomes]
rs12461099	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12461131	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12976571	0.82[ASN][1000 genomes]
rs12984383	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1366610	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1428922	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1457144	0.82[ASN][1000 genomes]
rs1870093	0.81[ASN][1000 genomes]
rs2075749	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2075750	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2075752	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2075754	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2290695	0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2305809	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs3786536	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3786538	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3810153	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3922888	0.83[ASN][1000 genomes]
rs4130852	0.83[ASN][1000 genomes]
rs4803511	0.83[ASN][1000 genomes]
rs4803512	0.83[ASN][1000 genomes]
rs58857981	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6509001	0.84[ASN][1000 genomes]
rs7248641	0.82[ASN][1000 genomes]
rs7250787	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7254214	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7257666	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7258163	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7259967	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73549152	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8102670	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8104958	0.82[ASN][1000 genomes]
rs8113780	0.82[ASN][1000 genomes]
rs873282	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs882520	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs891167	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs930102	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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
rs7259596	RABAC1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42365400-42369800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
2	chr19:42365400-42374800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr19:42365400-42375000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr19:42365400-42376200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr19:42365400-42376600	Genic enhancers	Primary B cells from peripheral blood	blood
6	chr19:42365600-42370000	Genic enhancers	Fetal Muscle Leg	muscle
7	chr19:42365600-42370800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr19:42365600-42374600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr19:42365600-42374800	Genic enhancers	Primary T cells fromperipheralblood	blood
10	chr19:42365800-42370800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr19:42365800-42374600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr19:42365800-42374800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr19:42365800-42375000	Genic enhancers	Fetal Intestine Small	intestine
14	chr19:42366000-42370800	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr19:42366000-42374800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
16	chr19:42366000-42376000	Strong transcription	HSMMtube	muscle
17	chr19:42366200-42370400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr19:42366200-42371000	Genic enhancers	Colonic Mucosa	Colon
19	chr19:42366400-42369800	Genic enhancers	Duodenum Smooth Muscle	Duodenum
20	chr19:42366400-42369800	Strong transcription	Placenta Amnion	Placenta Amnion
21	chr19:42366400-42377600	Strong transcription	Fetal Brain Female	brain
22	chr19:42366600-42374400	Strong transcription	Thymus	Thymus
23	chr19:42366600-42375000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr19:42366800-42370000	Strong transcription	ES-I3 Cell Line	embryonic stem cell
25	chr19:42366800-42370800	Genic enhancers	HMEC	breast
26	chr19:42366800-42374800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr19:42367000-42370400	Strong transcription	Fetal Muscle Trunk	muscle
28	chr19:42367000-42370800	Strong transcription	Fetal Lung	lung
29	chr19:42367000-42370800	Strong transcription	Rectal Smooth Muscle	rectum
30	chr19:42367000-42372000	Genic enhancers	Duodenum Mucosa	Duodenum
31	chr19:42367000-42373800	Weak transcription	Right Atrium	heart
32	chr19:42367000-42376600	Strong transcription	H9 Cell Line	embryonic stem cell
33	chr19:42367000-42376800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr19:42367200-42371000	Strong transcription	Brain Substantia Nigra	brain
35	chr19:42367200-42377200	Strong transcription	Brain Inferior Temporal Lobe	brain
36	chr19:42367400-42370800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr19:42367400-42371600	Strong transcription	Fetal Intestine Large	intestine
38	chr19:42367400-42372600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr19:42367400-42375600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr19:42367600-42370400	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr19:42367600-42370600	Genic enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr19:42367600-42370800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr19:42367600-42371400	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr19:42367600-42372400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr19:42367600-42374800	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr19:42367600-42374800	Genic enhancers	HepG2	liver
47	chr19:42367600-42375200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
48	chr19:42367600-42375600	Strong transcription	Right Ventricle	heart
49	chr19:42367600-42376200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr19:42367600-42379200	Weak transcription	Fetal Brain Male	brain

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