Variant report

Variant	rs1197659
Chromosome Location	chr15:42076387-42076388
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1043627	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.90[ASN][1000 genomes]
rs1106934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11070346	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11070349	0.95[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs11547012	0.95[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs11630242	0.86[ASN][1000 genomes]
rs11853665	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11858843	1.00[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs1197662	0.80[CHB][hapmap]
rs1197668	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs1197687	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1197688	0.93[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1197689	0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.95[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1197690	0.93[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1197770	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1197773	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1206842	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1209333	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12439771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12440605	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs12591285	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12595271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12901742	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16971915	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs1726915	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1918312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1918313	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]
rs2077361	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2077543	0.94[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs2241523	0.95[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs2412639	0.81[AMR][1000 genomes]
rs2412640	1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs2577949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28671571	0.88[ASN][1000 genomes]
rs2925340	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34769385	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35033220	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35359048	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3816533	0.86[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4072386	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs4923906	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4923907	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4923913	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4923917	0.95[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs4924573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57814590	0.85[ASN][1000 genomes]
rs7166139	0.95[CHB][hapmap];0.85[CHD][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs7168489	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7173779	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7174099	0.95[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs7175346	0.94[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs7177495	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8025614	0.82[JPT][hapmap]
rs8035855	0.81[JPT][hapmap]
rs883329	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs890504	0.83[ASN][1000 genomes]
rs9806709	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
3	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
4	nsv1054671	chr15:42016097-42098896	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1038894	chr15:42038152-42077452	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	esv2757597	chr15:42047173-42122617	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	esv2760027	chr15:42047173-42122617	Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	nsv904113	chr15:42050390-42118971	Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription 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 target site	19 gene(s)	inside rSNPs	diseases
9	nsv904114	chr15:42050390-42119900	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv427958	chr15:42051317-42301283	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
11	nsv904115	chr15:42076387-42171483	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
12	nsv904116	chr15:42076387-42229852	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1197659	JMJD7-PLA2G4B	cis	cerebellum	SCAN
rs1197659	ZFYVE19	cis	parietal	SCAN
rs1197659	NUSAP1	cis	cerebellum	SCAN
rs1197659	VPS18	cis	parietal	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42067600-42083000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr15:42068000-42078800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:42068200-42082600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr15:42068400-42081800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr15:42068600-42081600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr15:42069800-42081800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr15:42070000-42081600	Weak transcription	Aorta	Aorta
8	chr15:42070000-42082600	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr15:42070200-42109800	Weak transcription	Fetal Brain Male	brain
10	chr15:42071000-42082400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr15:42071000-42082800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr15:42071000-42092800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr15:42071200-42092000	Weak transcription	Brain Germinal Matrix	brain
14	chr15:42072400-42077400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr15:42072400-42080400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr15:42072400-42080800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr15:42072400-42081600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr15:42072600-42080600	Weak transcription	Primary T cells from cord blood	blood
19	chr15:42072600-42081200	Weak transcription	HSMMtube	muscle
20	chr15:42072600-42081800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr15:42072600-42081800	Weak transcription	NH-A	brain
22	chr15:42072600-42082600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr15:42072800-42080600	Weak transcription	Brain Anterior Caudate	brain
24	chr15:42072800-42080600	Weak transcription	Left Ventricle	heart
25	chr15:42072800-42080600	Weak transcription	Psoas Muscle	Psoas
26	chr15:42072800-42080600	Weak transcription	Right Ventricle	heart
27	chr15:42072800-42080800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr15:42072800-42081600	Weak transcription	Right Atrium	heart
29	chr15:42073000-42080800	Weak transcription	Stomach Smooth Muscle	stomach
30	chr15:42073000-42081000	Weak transcription	Adipose Nuclei	Adipose
31	chr15:42073000-42081200	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr15:42073000-42081400	Weak transcription	Fetal Stomach	stomach
33	chr15:42073000-42082600	Weak transcription	A549	lung
34	chr15:42073200-42080600	Weak transcription	Brain Angular Gyrus	brain
35	chr15:42073200-42080600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr15:42073200-42080600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr15:42073200-42080600	Weak transcription	Brain Substantia Nigra	brain
38	chr15:42073200-42080600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr15:42073200-42080800	Weak transcription	Colon Smooth Muscle	Colon
40	chr15:42073200-42082600	Weak transcription	Osteobl	bone
41	chr15:42073800-42076600	Enhancers	Fetal Intestine Large	intestine
42	chr15:42074000-42079800	Weak transcription	HUVEC	blood vessel
43	chr15:42074400-42076600	Enhancers	Primary B cells from peripheral blood	blood
44	chr15:42074600-42076600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr15:42075000-42076400	Enhancers	Fetal Heart	heart
46	chr15:42075000-42076400	Enhancers	HepG2	liver
47	chr15:42075000-42076600	Genic enhancers	Fetal Intestine Small	intestine
48	chr15:42075200-42076400	Enhancers	K562	blood
49	chr15:42075200-42076800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr15:42075400-42081000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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