Variant report

Variant	rs4887077
Chromosome Location	chr15:78978364-78978365
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:78977969..78980271-chr15:78982460..78985285,2	K562	blood:

Extended variants
information (count: 72 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1021071	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1051730	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11072785	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11072790	0.97[EUR][1000 genomes]
rs11072791	0.93[EUR][1000 genomes]
rs11072792	0.87[EUR][1000 genomes]
rs11629637	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11630236	1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[YRI][hapmap]
rs11631955	1.00[JPT][hapmap]
rs11633178	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634351	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634543	0.95[EUR][1000 genomes]
rs11638372	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638490	0.87[EUR][1000 genomes]
rs11638830	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11639044	0.84[MEX][hapmap];0.80[MKK][hapmap]
rs11639049	0.91[EUR][1000 genomes]
rs11639166	0.91[EUR][1000 genomes]
rs11639181	0.91[EUR][1000 genomes]
rs11639347	0.91[EUR][1000 genomes]
rs11639372	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11639375	0.91[EUR][1000 genomes]
rs11639382	0.91[EUR][1000 genomes]
rs12286	0.96[CEU][hapmap]
rs12899135	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12899147	0.84[MEX][hapmap]
rs12900168	0.88[CEU][hapmap];0.84[MEX][hapmap]
rs12901913	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12902602	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12910627	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs16969968	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17487223	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs17487514	0.89[MKK][hapmap]
rs1809420	0.92[CEU][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap]
rs1825082	0.91[EUR][1000 genomes]
rs1825083	0.91[EUR][1000 genomes]
rs1994016	0.84[MEX][hapmap]
rs1996371	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2036527	1.00[JPT][hapmap]
rs2170311	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2277550	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2869554	0.83[EUR][1000 genomes]
rs2869566	0.86[EUR][1000 genomes]
rs34225855	0.88[EUR][1000 genomes]
rs34563625	0.84[EUR][1000 genomes]
rs35583595	0.88[EUR][1000 genomes]
rs3813565	0.96[CEU][hapmap];0.89[GIH][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs3894347	0.80[EUR][1000 genomes]
rs4886579	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886580	0.95[EUR][1000 genomes]
rs4886587	0.84[EUR][1000 genomes]
rs4887082	1.00[CEU][hapmap]
rs4887086	0.85[EUR][1000 genomes]
rs4887087	0.86[EUR][1000 genomes]
rs6495314	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71448817	0.81[EUR][1000 genomes]
rs7171916	0.81[CEU][hapmap]
rs7174367	0.92[CEU][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap]
rs7180002	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs72743199	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8031948	1.00[JPT][hapmap]
rs8034191	1.00[JPT][hapmap]
rs922692	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs951266	1.00[CHB][hapmap];1.00[JPT][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	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	nsv1045827	chr15:78907656-79004642	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv457208	chr15:78908032-79019610	Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv570201	chr15:78908032-79019610	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv974713	chr15:78945824-78996783	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv457209	chr15:78949127-78986805	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv471256	chr15:78949127-78986805	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv570203	chr15:78949127-78986805	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4887077	CHRNA5	cis	cerebellum	SCAN
rs4887077	PSMA4	cis	parietal	SCAN
rs4887077	CHRNA5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78972000-78980000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr15:78976800-78979200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr15:78976800-78979200	Enhancers	Fetal Thymus	thymus
4	chr15:78976800-78979600	Enhancers	Fetal Kidney	kidney
5	chr15:78977000-78978800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr15:78977200-78978400	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr15:78977200-78978600	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr15:78977400-78978400	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr15:78977400-78978400	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr15:78977400-78978400	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr15:78977400-78978600	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr15:78977400-78978600	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr15:78977400-78978600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr15:78977400-78978600	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr15:78977400-78978800	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr15:78977400-78978800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr15:78977400-78979200	Enhancers	Adipose Nuclei	Adipose
18	chr15:78977400-78981200	Enhancers	Fetal Lung	lung
19	chr15:78977600-78978400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
20	chr15:78977600-78978400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr15:78977600-78978400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr15:78977600-78978400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr15:78977600-78978600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:78977600-78978600	Enhancers	Esophagus	oesophagus
25	chr15:78977600-78978800	Enhancers	H1 Cell Line	embryonic stem cell
26	chr15:78977600-78978800	Enhancers	Fetal Muscle Trunk	muscle
27	chr15:78977600-78978800	Enhancers	Fetal Stomach	stomach
28	chr15:78977600-78978800	Enhancers	Spleen	Spleen
29	chr15:78977600-78979000	Enhancers	Fetal Muscle Leg	muscle
30	chr15:78977600-78979000	Enhancers	Left Ventricle	heart
31	chr15:78977800-78978600	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr15:78977800-78980200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr15:78978000-78978400	Weak transcription	Fetal Brain Female	brain
34	chr15:78978000-78978400	Enhancers	Stomach Mucosa	stomach
35	chr15:78978000-78978600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr15:78978000-78978800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
37	chr15:78978200-78978600	Enhancers	H9 Cell Line	embryonic stem cell
38	chr15:78978200-78979000	Enhancers	Thymus	Thymus
39	chr15:78978200-78979800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr15:78978200-78980200	Weak transcription	HMEC	breast

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