Variant report

Variant	rs34040639
Chromosome Location	chr15:41760807-41760808
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	chr15:41760491..41765173-chr15:41766010..41771249,5	K562	blood:
2	chr15:41760653..41762830-chr15:41768772..41771249,2	K562	blood:

Variant related genes	Relation type
ENSG00000137815	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 25 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10518717	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11070328	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap]
rs11630656	0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[TSI][hapmap]
rs11630799	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11634582	1.00[JPT][hapmap]
rs11635906	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11854081	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11854632	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs11854820	0.86[EUR][1000 genomes]
rs11858068	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11858812	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13313520	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap]
rs1757468	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17676332	1.00[JPT][hapmap]
rs17677098	1.00[JPT][hapmap]
rs17730589	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap]
rs17730888	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap]
rs1899	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs2118740	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs2730056	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2730058	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28374715	1.00[CHB][hapmap]
rs28416360	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28421136	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28456082	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28459164	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28463309	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap]
rs28493702	0.93[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];0.91[TSI][hapmap]
rs28555198	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28557159	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs28576457	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28584379	0.87[EUR][1000 genomes]
rs28631111	1.00[CHB][hapmap]
rs28663426	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28673484	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28700583	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28703570	0.86[EUR][1000 genomes]
rs28897479	0.87[EUR][1000 genomes]
rs316604	0.93[CEU][hapmap];0.96[GIH][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs316606	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs316607	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs316611	0.86[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs316616	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3204853	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs34285452	0.85[EUR][1000 genomes]
rs34665396	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4924549	1.00[CHB][hapmap]
rs55725658	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6493003	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7164211	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7164684	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7165914	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap]
rs7168002	0.85[EUR][1000 genomes]
rs7168307	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs7168431	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs7169543	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap]
rs7181982	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs72739644	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8023530	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs8034840	0.85[EUR][1000 genomes]
rs8036026	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs8036734	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8037574	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs8041809	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9568	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs9646193	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933757	chr15:41641236-41773058	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases
2	nsv524476	chr15:41689232-41820200	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:25)

SNP	Gene	Cis/trans	Tissue	Source
rs34040639	SPINT1	cis	cerebellum	SCAN
rs34040639	LOC729082	Cis_1M	lymphoblastoid	RTeQTL
rs34040639	NDUFAF1	cis	lymphoblastoid	seeQTL
rs34040639	NDUFAF1	cis	Thyroid	GTEx
rs34040639	NDUFAF1	Cis_1M	lymphoblastoid	RTeQTL
rs34040639	RASGRP1	cis	cerebellum	SCAN
rs34040639	GPR176	cis	parietal	SCAN
rs34040639	NDUFAF1	cis	cerebellum	SCAN
rs34040639	OIP5-AS1	cis	Nerve Tibial	GTEx
rs34040639	NDUFAF1	cis	Esophagus Muscularis	GTEx
rs34040639	NUSAP1	cis	cerebellum	SCAN
rs34040639	NDUFAF1	cis	lung	GTEx
rs34040639	NDUFAF1	cis	multi-tissue	Pritchard
rs34040639	OIP5-AS1	cis	Adipose Subcutaneous	GTEx
rs34040639	GPR176	cis	cerebellum	SCAN
rs34040639	KRTAP4-7	Cis_1M	lymphoblastoid	RTeQTL
rs34040639	OIP5-AS1	cis	Artery Tibial	GTEx
rs34040639	RPAP1	cis	parietal	SCAN
rs34040639	NUSAP1	cis	parietal	SCAN
rs34040639	NDUFAF1	cis	Heart Left Ventricle	GTEx
rs34040639	NDUFAF1	cis	parietal	SCAN
rs34040639	OIP5-AS1	cis	Esophagus Mucosa	GTEx
rs34040639	ZFP106	cis	parietal	SCAN
rs34040639	NDUFAF1	cis	Muscle Skeletal	GTEx
rs34040639	NDUFAF1	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41719000-41765800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:41722000-41768400	Weak transcription	Small Intestine	intestine
3	chr15:41724200-41777200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:41729200-41773000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr15:41730000-41768400	Weak transcription	Psoas Muscle	Psoas
6	chr15:41730800-41769000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr15:41743800-41762200	Weak transcription	Stomach Mucosa	stomach
8	chr15:41744000-41771800	Strong transcription	Fetal Intestine Small	intestine
9	chr15:41744200-41767400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr15:41745200-41766800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr15:41745200-41775800	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr15:41745800-41763400	Weak transcription	Pancreas	Pancrea
13	chr15:41748000-41761000	Weak transcription	A549	lung
14	chr15:41750600-41761200	Weak transcription	Right Ventricle	heart
15	chr15:41750600-41761800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr15:41750600-41762200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr15:41750600-41766200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr15:41750800-41762200	Weak transcription	NHLF	lung
19	chr15:41750800-41763000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr15:41750800-41763400	Weak transcription	Aorta	Aorta
21	chr15:41750800-41767000	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr15:41753000-41775000	Strong transcription	Fetal Stomach	stomach
23	chr15:41753800-41764000	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr15:41753800-41776800	Strong transcription	Fetal Muscle Leg	muscle
25	chr15:41754000-41764800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr15:41754000-41774400	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr15:41754200-41764000	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr15:41754200-41775200	Strong transcription	Primary T cells from cord blood	blood
29	chr15:41754200-41776000	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr15:41754400-41764000	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr15:41754400-41774600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr15:41754400-41775000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr15:41754400-41776800	Strong transcription	Placenta	Placenta
34	chr15:41754600-41764000	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr15:41754600-41764000	Strong transcription	Adipose Nuclei	Adipose
36	chr15:41754600-41766800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr15:41755000-41769400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr15:41755000-41775600	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr15:41755400-41775200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr15:41756000-41761200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr15:41756800-41763800	Strong transcription	Duodenum Mucosa	Duodenum
42	chr15:41756800-41764000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr15:41756800-41764000	Strong transcription	Dnd41	blood
44	chr15:41756800-41764000	Strong transcription	GM12878-XiMat	blood
45	chr15:41756800-41769000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr15:41756800-41776200	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr15:41757000-41764000	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr15:41757000-41764200	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr15:41757000-41764800	Strong transcription	Liver	Liver
50	chr15:41757000-41769000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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