Variant report

Variant	rs1918313
Chromosome Location	chr15:42005772-42005773
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	chr15:41987539..41989124-chr15:42004942..42006906,2	K562	blood:
2	chr15:42005381..42008216-chr15:42025990..42028220,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000174197	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1043627	0.93[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.83[ASN][1000 genomes]
rs1106934	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.87[YRI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11070346	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11070349	0.90[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs11547012	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs11853665	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11858843	0.95[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs1197659	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1197668	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs1197687	0.93[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.83[ASN][1000 genomes]
rs1197688	0.93[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.83[ASN][1000 genomes]
rs1197689	0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1197690	0.93[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1197770	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1197773	0.93[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1206842	0.85[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.83[ASN][1000 genomes]
rs1209333	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12439771	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12440605	0.95[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs12591285	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12595271	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12901742	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16971915	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1726915	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1918312	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2077361	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2077543	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs2241523	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs2412640	0.95[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap]
rs2577949	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28671571	0.80[ASN][1000 genomes]
rs2925340	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs34769385	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35033220	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35359048	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3816533	0.86[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.81[ASN][1000 genomes]
rs4072386	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs4923906	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4923907	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4923913	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4923917	0.90[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap]
rs4924573	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57814590	0.90[ASN][1000 genomes]
rs7166139	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs7168489	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7173779	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.80[ASN][1000 genomes]
rs7174099	0.90[CHB][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs7175346	0.88[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs7177495	0.93[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8025614	0.82[JPT][hapmap]
rs8035855	0.81[JPT][hapmap]
rs9806709	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049514	chr15:41958482-42081210	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1048655	chr15:41978391-42049360	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
4	nsv1036086	chr15:42004962-42091451	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers 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 target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1918313	NUSAP1	cis	cerebellum	SCAN
rs1918313	JMJD7-PLA2G4B	cis	cerebellum	SCAN
rs1918313	VPS18	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41972400-42065200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:41984200-42034800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:41989000-42041600	Weak transcription	Fetal Brain Male	brain
4	chr15:41989200-42009400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr15:41991800-42006000	Weak transcription	HMEC	breast
6	chr15:41995000-42007200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr15:41995400-42023800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr15:41995800-42006400	Strong transcription	Fetal Muscle Leg	muscle
9	chr15:41996000-42007000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr15:41996200-42034800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr15:41997000-42006600	Strong transcription	Hela-S3	cervix
12	chr15:41997400-42006200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr15:41997400-42006400	Strong transcription	Primary T helper cells PMA-I stimulated	--
14	chr15:41997400-42006600	Strong transcription	Primary B cells from cord blood	blood
15	chr15:41997400-42006600	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr15:41997400-42008400	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr15:41997400-42008800	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr15:41997600-42006200	Strong transcription	Fetal Thymus	thymus
19	chr15:41997600-42007200	Strong transcription	Primary B cells from peripheral blood	blood
20	chr15:41998000-42008400	Weak transcription	NHLF	lung
21	chr15:41998600-42006600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr15:41998600-42006800	Strong transcription	Fetal Muscle Trunk	muscle
23	chr15:41998800-42006600	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr15:41999000-42006800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:41999000-42008200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr15:41999200-42006800	Strong transcription	Primary hematopoietic stem cells	blood
27	chr15:41999200-42008200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr15:41999400-42006200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr15:41999400-42006200	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr15:41999400-42006400	Strong transcription	Placenta	Placenta
31	chr15:41999400-42006400	Strong transcription	Thymus	Thymus
32	chr15:41999400-42006600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr15:41999400-42006600	Strong transcription	Primary T cells from cord blood	blood
34	chr15:41999400-42006600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr15:41999400-42006600	Strong transcription	Liver	Liver
36	chr15:41999400-42006800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr15:41999400-42006800	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr15:41999400-42006800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr15:41999400-42006800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr15:41999400-42007200	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr15:41999600-42006000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr15:41999600-42006200	Strong transcription	Fetal Brain Female	brain
43	chr15:41999600-42006600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr15:41999600-42006600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr15:41999600-42006600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr15:41999600-42006800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr15:41999600-42007000	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr15:41999800-42006800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr15:41999800-42018400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr15:42000000-42006600	Strong transcription	Osteobl	bone

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