Variant report

Variant	rs8042411
Chromosome Location	chr15:55485494-55485495
allele	A/G
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:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:55484699..55490442-chr15:55579270..55584640,8	K562	blood:
2	chr15:55482890..55486340-chr15:55487631..55490505,4	MCF-7	breast:
3	chr15:55475644..55477997-chr15:55484003..55486160,2	MCF-7	breast:
4	chr15:55463428..55465333-chr15:55485353..55487968,3	K562	blood:
5	chr15:55485173..55489207-chr15:55609824..55611374,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PIGB-2	chr15:55485456-55485554	ucscGeneNc_uc002aeh_2

No data

Variant related genes	Relation type
ENSG00000225973	Chromatin interaction
ENSG00000137876	Chromatin interaction
ENSG00000069943	Chromatin interaction
ENSG00000069974	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10047995	0.97[EUR][1000 genomes]
rs10152400	0.97[EUR][1000 genomes]
rs10518800	0.94[EUR][1000 genomes]
rs11852793	0.94[EUR][1000 genomes]
rs11853315	0.81[EUR][1000 genomes]
rs11855084	1.00[CEU][hapmap]
rs11855490	1.00[CEU][hapmap];0.90[GIH][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs11857829	1.00[CEU][hapmap]
rs11858001	0.97[EUR][1000 genomes]
rs16976069	0.94[EUR][1000 genomes]
rs16976076	0.94[EUR][1000 genomes]
rs2414403	0.97[EUR][1000 genomes]
rs28565375	0.94[EUR][1000 genomes]
rs524935	0.94[EUR][1000 genomes]
rs58922764	0.97[EUR][1000 genomes]
rs59357544	0.94[EUR][1000 genomes]
rs59683414	0.92[EUR][1000 genomes]
rs60802234	0.97[EUR][1000 genomes]
rs6493764	0.97[EUR][1000 genomes]
rs6493765	0.97[EUR][1000 genomes]
rs7163677	0.97[EUR][1000 genomes]
rs7168226	0.92[EUR][1000 genomes]
rs7169357	0.97[EUR][1000 genomes]
rs73404044	0.86[EUR][1000 genomes]
rs73404055	0.86[EUR][1000 genomes]
rs73404072	0.94[EUR][1000 genomes]
rs73404076	0.94[EUR][1000 genomes]
rs73404078	0.94[EUR][1000 genomes]
rs73404093	0.94[EUR][1000 genomes]
rs73405810	0.97[EUR][1000 genomes]
rs73405811	0.97[EUR][1000 genomes]
rs73405825	0.97[EUR][1000 genomes]
rs73405883	0.97[EUR][1000 genomes]
rs73405887	0.97[EUR][1000 genomes]
rs73405889	0.97[EUR][1000 genomes]
rs73405890	0.97[EUR][1000 genomes]
rs73405894	0.94[EUR][1000 genomes]
rs73405895	0.94[EUR][1000 genomes]
rs73405898	0.97[EUR][1000 genomes]
rs73407806	0.94[EUR][1000 genomes]
rs73407807	0.94[EUR][1000 genomes]
rs73407809	0.94[EUR][1000 genomes]
rs73407811	0.94[EUR][1000 genomes]
rs73407814	0.94[EUR][1000 genomes]
rs73407815	0.94[EUR][1000 genomes]
rs73407816	0.94[EUR][1000 genomes]
rs73407817	0.94[EUR][1000 genomes]
rs73407821	0.97[EUR][1000 genomes]
rs73407823	0.97[EUR][1000 genomes]
rs73407850	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73409840	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs74015506	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs74018312	0.92[EUR][1000 genomes]
rs8026190	0.86[EUR][1000 genomes]
rs8038091	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043176	chr15:55010228-55563000	Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1042741	chr15:55068022-55622497	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1039471	chr15:55137606-55552555	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
6	nsv525768	chr15:55466155-55485494	Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8042411	RAB27A	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55455800-55487200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:55462600-55488600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:55464800-55488200	Weak transcription	Lung	lung
4	chr15:55466800-55486800	Weak transcription	Psoas Muscle	Psoas
5	chr15:55468800-55487000	Weak transcription	Gastric	stomach
6	chr15:55469600-55486000	Strong transcription	Primary B cells from cord blood	blood
7	chr15:55469800-55486400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:55469800-55486600	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr15:55470200-55486600	Weak transcription	Small Intestine	intestine
10	chr15:55470400-55486400	Strong transcription	Primary B cells from peripheral blood	blood
11	chr15:55470400-55486400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr15:55470800-55485800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr15:55471000-55486000	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr15:55471000-55486200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr15:55471000-55487000	Weak transcription	Pancreas	Pancrea
16	chr15:55471400-55485800	Weak transcription	Stomach Mucosa	stomach
17	chr15:55471600-55486800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr15:55472000-55486200	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr15:55472200-55488000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr15:55472400-55488400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr15:55472600-55488400	Weak transcription	Esophagus	oesophagus
22	chr15:55473000-55487000	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr15:55473000-55487400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr15:55473000-55487600	Weak transcription	Aorta	Aorta
25	chr15:55473600-55486800	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr15:55474200-55486200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr15:55475000-55487400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr15:55476600-55485600	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr15:55477200-55485600	Strong transcription	A549	lung
30	chr15:55477200-55486400	Weak transcription	Fetal Brain Male	brain
31	chr15:55477200-55486400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr15:55477200-55487000	Weak transcription	Thymus	Thymus
33	chr15:55477200-55487200	Weak transcription	Fetal Kidney	kidney
34	chr15:55478200-55486400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr15:55479000-55486400	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr15:55480200-55486400	Strong transcription	HMEC	breast
37	chr15:55480600-55485800	Strong transcription	Fetal Thymus	thymus
38	chr15:55480600-55486200	Strong transcription	HSMM	muscle
39	chr15:55481600-55486800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr15:55481800-55487600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr15:55482200-55486400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr15:55482200-55486400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr15:55482200-55487600	Weak transcription	Brain Substantia Nigra	brain
44	chr15:55482200-55488000	Weak transcription	Left Ventricle	heart
45	chr15:55482400-55486400	Weak transcription	Right Ventricle	heart
46	chr15:55482400-55487000	Weak transcription	Spleen	Spleen
47	chr15:55482400-55487800	Weak transcription	Fetal Intestine Small	intestine
48	chr15:55482400-55488400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr15:55482600-55485600	Strong transcription	K562	blood
50	chr15:55482600-55485800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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