Variant report

Variant	rs4774750
Chromosome Location	chr15:55466155-55466156
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	chr10:13366886..13368696-chr15:55465125..55467342,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RSL24D1-1	chr15:55464171-55468937	ENSG00000248800

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1050931	0.81[CHB][hapmap];0.87[GIH][hapmap]
rs10518801	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1061823	0.81[CHB][hapmap]
rs1061824	0.81[CHB][hapmap];0.87[GIH][hapmap]
rs1061870	0.81[CHB][hapmap];0.87[GIH][hapmap]
rs1061873	0.81[CHB][hapmap];0.87[GIH][hapmap]
rs11071165	0.87[CEU][hapmap]
rs11071168	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11071172	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071173	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16976036	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs16976039	0.81[CHB][hapmap]
rs16976149	0.81[CHB][hapmap]
rs2572034	0.81[EUR][1000 genomes]
rs2641583	0.87[EUR][1000 genomes]
rs28524517	0.94[ASN][1000 genomes]
rs28589384	0.81[CHB][hapmap];0.87[GIH][hapmap]
rs28670780	0.94[ASN][1000 genomes]
rs2899580	0.81[CHB][hapmap]
rs2899582	0.81[CHB][hapmap]
rs3179664	0.81[CHB][hapmap]
rs3759861	0.87[CHB][hapmap];0.87[GIH][hapmap]
rs3759862	0.87[CHB][hapmap]
rs3809539	0.81[CHB][hapmap]
rs3809540	0.87[CHB][hapmap];0.80[CHD][hapmap];0.87[GIH][hapmap]
rs4774751	1.00[ASN][1000 genomes]
rs486913	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs508482	0.87[EUR][1000 genomes]
rs559069	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6493767	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6493768	0.87[CHB][hapmap]
rs7168057	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7168472	0.87[CHB][hapmap]
rs7169407	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7172575	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8027098	0.81[CHB][hapmap]
rs8031949	0.81[CHB][hapmap]
rs8034402	0.87[CHB][hapmap]
rs8034882	0.87[CHB][hapmap]
rs8035625	0.87[CHB][hapmap]
rs8043029	0.87[CHB][hapmap];0.80[CHD][hapmap];0.87[GIH][hapmap]
rs9300	0.87[CHB][hapmap];0.80[CHD][hapmap];0.87[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv457156	chr15:55400649-55466155	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv569521	chr15:55400649-55466155	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	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
8	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4774750	RAB27A	Cis_1M	lymphoblastoid	RTeQTL
rs4774750	RAB27A	cis	lymphoblastoid	seeQTL
rs4774750	RSL24D1	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55455600-55469600	Weak transcription	Aorta	Aorta
2	chr15:55455800-55487200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:55459000-55469800	Weak transcription	HSMM	muscle
4	chr15:55461000-55469200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr15:55462600-55470200	Weak transcription	Fetal Lung	lung
6	chr15:55462600-55471600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr15:55462600-55488600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr15:55463200-55470400	Weak transcription	A549	lung
9	chr15:55463200-55472400	Weak transcription	Ovary	ovary
10	chr15:55463200-55474600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr15:55463400-55466200	Weak transcription	Psoas Muscle	Psoas
12	chr15:55463400-55472200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr15:55463800-55472600	Weak transcription	Fetal Kidney	kidney
14	chr15:55464000-55470800	Weak transcription	Brain Germinal Matrix	brain
15	chr15:55464400-55469000	Weak transcription	Primary T cells from cord blood	blood
16	chr15:55464400-55470600	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr15:55464600-55472400	Weak transcription	Brain Hippocampus Middle	brain
18	chr15:55464800-55488200	Weak transcription	Lung	lung
19	chr15:55465000-55469600	Weak transcription	Primary B cells from cord blood	blood
20	chr15:55465200-55470400	Weak transcription	Primary B cells from peripheral blood	blood
21	chr15:55465200-55470800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr15:55465400-55469800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr15:55465400-55469800	Weak transcription	Duodenum Mucosa	Duodenum
24	chr15:55465400-55470400	Weak transcription	Dnd41	blood
25	chr15:55465400-55470800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr15:55465400-55471000	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr15:55465400-55471200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr15:55465400-55471400	Weak transcription	Brain Angular Gyrus	brain
29	chr15:55465400-55472600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr15:55465400-55476600	Weak transcription	Brain Anterior Caudate	brain
31	chr15:55465600-55470000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr15:55465600-55470000	Weak transcription	Adipose Nuclei	Adipose
33	chr15:55465600-55470200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr15:55465600-55470400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr15:55465600-55470400	Weak transcription	Left Ventricle	heart
36	chr15:55465800-55467400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr15:55465800-55469400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr15:55465800-55470200	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr15:55465800-55471600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr15:55466000-55469200	Weak transcription	Liver	Liver

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