Variant report

Variant	rs972158
Chromosome Location	chr7:26335007-26335008
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:26224941..26227535-chr7:26333597..26335223,2	K562	blood:
2	chr7:26331702..26333313-chr7:26334773..26336506,2	MCF-7	breast:
3	chr7:26239911..26241819-chr7:26331558..26335355,4	K562	blood:
4	chr7:26240319..26241875-chr7:26333855..26336720,2	K562	blood:
5	chr7:26238219..26243115-chr7:26329445..26335775,8	MCF-7	breast:
6	chr7:26238789..26244149-chr7:26328226..26335284,15	MCF-7	breast:

Variant related genes	Relation type
ENSG00000086300	Chromatin interaction
ENSG00000122565	Chromatin interaction
ENSG00000122566	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10273457	0.81[EUR][1000 genomes]
rs10275783	0.96[CEU][hapmap];0.80[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11525780	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs12538243	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13222190	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs13227895	0.84[EUR][1000 genomes]
rs13228053	0.82[EUR][1000 genomes]
rs13229994	0.86[EUR][1000 genomes]
rs17153429	0.89[CEU][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs2562786	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2562795	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28653301	0.86[EUR][1000 genomes]
rs28682465	0.86[EUR][1000 genomes]
rs33974860	0.86[EUR][1000 genomes]
rs34272723	0.86[EUR][1000 genomes]
rs34695308	0.86[EUR][1000 genomes]
rs67157703	0.81[EUR][1000 genomes]
rs6975395	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs7794280	0.82[ASW][hapmap]
rs9639532	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs972158	NUPL2	cis	cerebellum	SCAN
rs972158	GPNMB	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26332400-26347000	Weak transcription	HMEC	breast
2	chr7:26332600-26337200	Weak transcription	Lung	lung
3	chr7:26332600-26347400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:26332600-26347400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr7:26332800-26335600	Weak transcription	Fetal Brain Male	brain
6	chr7:26332800-26342000	Weak transcription	Fetal Intestine Small	intestine
7	chr7:26332800-26343000	Weak transcription	Spleen	Spleen
8	chr7:26332800-26346200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr7:26332800-26346400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr7:26332800-26346600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr7:26333400-26335200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr7:26333400-26344600	Weak transcription	Placenta	Placenta
13	chr7:26333600-26346600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr7:26333600-26351400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr7:26333800-26335400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr7:26333800-26346800	Weak transcription	Pancreas	Pancrea
17	chr7:26334000-26335200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr7:26334000-26337800	Weak transcription	Liver	Liver
19	chr7:26334000-26338400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr7:26334000-26341000	Weak transcription	HepG2	liver
21	chr7:26334200-26335200	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr7:26334200-26335200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr7:26334200-26335400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr7:26334200-26338600	Genic enhancers	Primary B cells from peripheral blood	blood
25	chr7:26334200-26346200	Weak transcription	K562	blood
26	chr7:26334400-26335200	Enhancers	Primary hematopoietic stem cells	blood
27	chr7:26334400-26335200	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr7:26334400-26335400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr7:26334400-26341000	Weak transcription	Brain Angular Gyrus	brain
30	chr7:26334600-26335200	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr7:26334600-26335200	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr7:26334600-26340200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr7:26334600-26344800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr7:26334600-26344800	Weak transcription	Thymus	Thymus
35	chr7:26334800-26335200	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr7:26334800-26337400	Genic enhancers	Primary B cells from cord blood	blood
37	chr7:26334800-26340800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr7:26335000-26336000	Genic enhancers	Monocytes-CD14+_RO01746	blood
39	chr7:26335000-26336200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr7:26335000-26340600	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr7:26335000-26340800	Weak transcription	Primary T cells from cord blood	blood
42	chr7:26335000-26344600	Weak transcription	Fetal Thymus	thymus
43	chr7:26335000-26344800	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr7:26335000-26353000	Weak transcription	GM12878-XiMat	blood

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