Variant report

Variant	rs17153429
Chromosome Location	chr7:26340970-26340971
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:26337033..26341522-chr7:26343910..26346140,5	K562	blood:
2	chr7:26335516..26340174-chr7:26340453..26343647,5	K562	blood:
3	chr7:26339720..26342269-chr7:26343705..26346837,3	MCF-7	breast:
4	chr7:26340483..26343827-chr7:26348426..26350723,3	K562	blood:
5	chr7:26335544..26340174-chr7:26340481..26343647,5	K562	blood:
6	chr7:26340732..26342659-chr7:26342750..26344382,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10227678	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10236496	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10273457	0.89[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10275783	0.89[CEU][hapmap]
rs10464319	0.82[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs10499574	0.82[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.94[MKK][hapmap];0.89[ASN][1000 genomes]
rs11525780	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs12671127	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12700720	0.89[CEU][hapmap];1.00[GIH][hapmap];0.86[TSI][hapmap]
rs13222190	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13223339	0.86[ASN][1000 genomes]
rs13223506	0.86[ASN][1000 genomes]
rs13227895	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13228053	0.83[EUR][1000 genomes]
rs13229994	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13233547	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13238680	0.86[ASN][1000 genomes]
rs13243412	0.86[ASN][1000 genomes]
rs2562786	0.86[EUR][1000 genomes]
rs2562795	0.83[EUR][1000 genomes]
rs28413943	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28653301	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28682465	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs33974860	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34272723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34315589	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34319640	0.87[ASN][1000 genomes]
rs34695308	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34809078	0.84[ASN][1000 genomes]
rs34822078	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs35255654	0.86[ASN][1000 genomes]
rs35424926	0.84[ASN][1000 genomes]
rs4722590	0.82[CEU][hapmap];0.80[CHB][hapmap];0.86[CHD][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs62448361	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs67157703	0.80[EUR][1000 genomes]
rs67229315	0.82[EUR][1000 genomes]
rs6953792	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6970361	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6975395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9638833	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9639532	0.88[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9648323	0.91[ASW][hapmap];0.89[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs972158	0.89[CEU][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021308	chr7:26116605-26419720	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv1018971	chr7:26161228-26380361	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	nsv1018352	chr7:26298095-26341825	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1029596	chr7:26302739-26737913	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv538804	chr7:26302739-26737913	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	esv2761313	chr7:26340970-26389772	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17153429	GPNMB	cis	cerebellum	SCAN
rs17153429	GPNMB	cis	parietal	SCAN
rs17153429	NUPL2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26332400-26347000	Weak transcription	HMEC	breast
2	chr7:26332600-26347400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:26332600-26347400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr7:26332800-26342000	Weak transcription	Fetal Intestine Small	intestine
5	chr7:26332800-26343000	Weak transcription	Spleen	Spleen
6	chr7:26332800-26346200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr7:26332800-26346400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr7:26332800-26346600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr7:26333400-26344600	Weak transcription	Placenta	Placenta
10	chr7:26333600-26346600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr7:26333600-26351400	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr7:26333800-26346800	Weak transcription	Pancreas	Pancrea
13	chr7:26334000-26341000	Weak transcription	HepG2	liver
14	chr7:26334200-26346200	Weak transcription	K562	blood
15	chr7:26334400-26341000	Weak transcription	Brain Angular Gyrus	brain
16	chr7:26334600-26344800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr7:26334600-26344800	Weak transcription	Thymus	Thymus
18	chr7:26335000-26344600	Weak transcription	Fetal Thymus	thymus
19	chr7:26335000-26344800	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr7:26335000-26353000	Weak transcription	GM12878-XiMat	blood
21	chr7:26335200-26342200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr7:26335200-26344800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr7:26335200-26344800	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr7:26335200-26344800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr7:26335200-26386400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr7:26335400-26343200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr7:26338400-26341000	Weak transcription	Liver	Liver
28	chr7:26338600-26343200	Strong transcription	Primary B cells from peripheral blood	blood
29	chr7:26339000-26342400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr7:26339800-26342600	Genic enhancers	Primary monocytes fromperipheralblood	blood
31	chr7:26339800-26343200	Genic enhancers	Primary neutrophils fromperipheralblood	blood
32	chr7:26340000-26342600	Strong transcription	Primary hematopoietic stem cells	blood
33	chr7:26340200-26341400	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr7:26340200-26342600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr7:26340200-26343000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr7:26340600-26342200	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr7:26340600-26342600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr7:26340600-26343000	Strong transcription	Primary B cells from cord blood	blood
39	chr7:26340800-26341000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr7:26340800-26342000	Strong transcription	Primary T cells from cord blood	blood

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