Variant report

Variant	rs16976149
Chromosome Location	chr15:55485763-55485764
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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	chr15:55485508..55492313-chr15:55579801..55583590,12	K562	blood:
4	chr15:55475644..55477997-chr15:55484003..55486160,2	MCF-7	breast:
5	chr15:55463428..55465333-chr15:55485353..55487968,3	K562	blood:
6	chr15:55485173..55489207-chr15:55609824..55611374,3	K562	blood:

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

Extended variants
information (count: 93 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10162819	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10162843	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1050931	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs10518804	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1061821	0.80[ASN][1000 genomes]
rs1061822	0.84[ASN][1000 genomes]
rs1061823	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs1061824	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs1061870	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs1061873	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs1061874	0.80[ASN][1000 genomes]
rs1061875	0.80[ASN][1000 genomes]
rs11852763	0.84[ASN][1000 genomes]
rs11855907	0.84[ASN][1000 genomes]
rs11855973	0.84[ASN][1000 genomes]
rs11855978	0.82[ASN][1000 genomes]
rs11857087	0.93[ASN][1000 genomes]
rs12385963	0.93[ASN][1000 genomes]
rs12385965	0.85[YRI][hapmap]
rs13380400	0.84[ASN][1000 genomes]
rs13733	0.90[ASN][1000 genomes]
rs16976036	1.00[CHB][hapmap];0.80[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs16976039	0.87[ASW][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs16976065	0.94[ASN][1000 genomes]
rs16976083	0.94[ASN][1000 genomes]
rs16976094	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16976116	0.92[ASN][1000 genomes]
rs2289059	0.93[MKK][hapmap];0.85[YRI][hapmap]
rs28433503	0.82[ASN][1000 genomes]
rs28449712	0.82[ASN][1000 genomes]
rs28489312	0.84[ASN][1000 genomes]
rs28508034	0.82[ASN][1000 genomes]
rs28526269	0.82[ASN][1000 genomes]
rs28530662	0.82[ASN][1000 genomes]
rs28535372	0.82[ASN][1000 genomes]
rs28541469	0.82[ASN][1000 genomes]
rs28558576	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28562431	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28564077	0.83[ASN][1000 genomes]
rs28589384	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs28591259	0.82[ASN][1000 genomes]
rs28592928	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28600759	0.90[ASN][1000 genomes]
rs28630909	0.82[ASN][1000 genomes]
rs28636526	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28649719	0.82[ASN][1000 genomes]
rs28673043	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28699327	0.82[ASN][1000 genomes]
rs28704109	0.84[ASN][1000 genomes]
rs28706531	0.93[ASN][1000 genomes]
rs28708989	0.82[ASN][1000 genomes]
rs28710976	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28714578	0.84[ASN][1000 genomes]
rs2899580	0.85[CHB][hapmap];0.84[ASN][1000 genomes]
rs2899581	0.84[ASN][1000 genomes]
rs2899582	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs3179664	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs3759861	0.93[CHB][hapmap];0.91[ASN][1000 genomes]
rs3759862	0.93[CHB][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs3809539	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3809540	0.93[CHB][hapmap];0.90[ASN][1000 genomes]
rs4238316	0.98[ASN][1000 genomes]
rs4503734	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4545742	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4632077	0.84[CEU][hapmap];0.86[CHB][hapmap];0.85[YRI][hapmap]
rs62020115	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6493767	0.81[CHB][hapmap]
rs6493768	0.93[CHB][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs7165491	0.82[ASN][1000 genomes]
rs7168472	0.92[CEU][hapmap];0.93[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7168737	0.82[ASN][1000 genomes]
rs7172108	0.82[ASN][1000 genomes]
rs7172289	0.82[ASN][1000 genomes]
rs7179365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7180504	0.85[YRI][hapmap]
rs7180594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8027098	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs8030981	0.82[ASN][1000 genomes]
rs8031949	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs8033588	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8034063	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8034402	0.92[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8034853	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8034882	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.88[JPT][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8035625	0.85[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8043029	0.93[CHB][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs9300	0.93[CHB][hapmap];0.90[ASN][1000 genomes]
rs9920165	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16976149	RAB27A	cis	cerebellum	SCAN
rs16976149	RSL24D1	cis	parietal	SCAN
rs16976149	RSL24D1	cis	cerebellum	SCAN

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	chr15:55477200-55486400	Weak transcription	Fetal Brain Male	brain
29	chr15:55477200-55486400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr15:55477200-55487000	Weak transcription	Thymus	Thymus
31	chr15:55477200-55487200	Weak transcription	Fetal Kidney	kidney
32	chr15:55478200-55486400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr15:55479000-55486400	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr15:55480200-55486400	Strong transcription	HMEC	breast
35	chr15:55480600-55485800	Strong transcription	Fetal Thymus	thymus
36	chr15:55480600-55486200	Strong transcription	HSMM	muscle
37	chr15:55481600-55486800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr15:55481800-55487600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr15:55482200-55486400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr15:55482200-55486400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr15:55482200-55487600	Weak transcription	Brain Substantia Nigra	brain
42	chr15:55482200-55488000	Weak transcription	Left Ventricle	heart
43	chr15:55482400-55486400	Weak transcription	Right Ventricle	heart
44	chr15:55482400-55487000	Weak transcription	Spleen	Spleen
45	chr15:55482400-55487800	Weak transcription	Fetal Intestine Small	intestine
46	chr15:55482400-55488400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr15:55482600-55485800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr15:55482600-55487200	Weak transcription	Fetal Stomach	stomach
49	chr15:55483800-55486800	Weak transcription	NHDF-Ad	bronchial
50	chr15:55484000-55486000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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