Variant report

Variant	rs6540961
Chromosome Location	chr1:9650729-9650730
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:9601186..9603227-chr1:9650193..9652008,2	K562	blood:
2	chr1:9636153..9639901-chr1:9648602..9651962,4	K562	blood:
3	chr1:9650072..9650968-chr1:9686876..9687637,2	MCF-7	breast:
4	chr1:9597937..9599836-chr1:9648693..9652829,4	K562	blood:
5	chr1:9647686..9650205-chr1:9650359..9652937,2	MCF-7	breast:
6	chr1:9597781..9602686-chr1:9646599..9652829,9	K562	blood:

Variant related genes	Relation type
ENSG00000171612	Chromatin interaction
ENSG00000188807	Chromatin interaction
ENSG00000231181	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10864429	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12022881	0.81[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.87[ASN][1000 genomes]
rs12023288	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs12037667	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.96[TSI][hapmap];0.87[ASN][1000 genomes]
rs12040542	0.94[ASW][hapmap];0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.87[ASN][1000 genomes]
rs12045459	0.83[EUR][1000 genomes]
rs12045493	0.84[EUR][1000 genomes]
rs12070568	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12084279	0.86[ASN][1000 genomes]
rs28719694	0.86[EUR][1000 genomes]
rs3923984	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4073710	0.88[CEU][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs4074744	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4244632	0.80[JPT][hapmap]
rs4423053	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs4926482	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55655211	0.87[ASN][1000 genomes]
rs55687246	0.85[ASN][1000 genomes]
rs55780537	0.87[ASN][1000 genomes]
rs55986711	0.87[ASN][1000 genomes]
rs56026893	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56053581	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57272167	0.89[AFR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58478478	0.86[ASN][1000 genomes]
rs60744607	0.86[ASN][1000 genomes]
rs6540962	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6675436	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6698575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72646709	0.87[ASN][1000 genomes]
rs72646712	0.87[ASN][1000 genomes]
rs72646713	0.87[ASN][1000 genomes]
rs72646715	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72646718	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7411273	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7525099	0.86[ASN][1000 genomes]
rs7544083	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9430152	1.00[CEU][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9430153	1.00[CEU][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs9430174	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9430180	0.92[EUR][1000 genomes]
rs9430181	0.82[ASN][1000 genomes]
rs9430182	0.83[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9430183	0.81[ASN][1000 genomes]
rs9430184	0.83[CEU][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9430273	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9430274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9430332	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]

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	nsv931984	chr1:8879337-9694749	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers 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	570 gene(s)	inside rSNPs	diseases
2	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
3	nsv1013224	chr1:9441040-9699768	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv464283	chr1:9495571-9677853	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv545363	chr1:9495571-9677853	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv871521	chr1:9640291-9666364	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6540961	NPPA	cis	cerebellum	SCAN
rs6540961	HNRNPCL1	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9649400-9650800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
2	chr1:9649400-9651000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
3	chr1:9649400-9651000	Flanking Active TSS	Stomach Smooth Muscle	stomach
4	chr1:9649400-9652400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
5	chr1:9649600-9650800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:9649600-9650800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:9649600-9650800	Flanking Active TSS	Brain Cingulate Gyrus	brain
8	chr1:9649600-9650800	Flanking Active TSS	Brain Hippocampus Middle	brain
9	chr1:9649600-9650800	Flanking Active TSS	Fetal Muscle Leg	muscle
10	chr1:9649600-9650800	Flanking Active TSS	K562	blood
11	chr1:9649600-9651000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:9649600-9651400	Flanking Active TSS	Brain Germinal Matrix	brain
13	chr1:9649600-9652000	Flanking Active TSS	Brain Angular Gyrus	brain
14	chr1:9649600-9652000	Flanking Active TSS	Fetal Brain Female	brain
15	chr1:9649800-9650800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:9649800-9650800	Flanking Active TSS	Hela-S3	cervix
17	chr1:9649800-9650800	Flanking Active TSS	HepG2	liver
18	chr1:9649800-9651000	Flanking Active TSS	Brain Anterior Caudate	brain
19	chr1:9649800-9651800	Enhancers	Primary B cells from peripheral blood	blood
20	chr1:9649800-9651800	Enhancers	Ovary	ovary
21	chr1:9649800-9652000	Flanking Active TSS	GM12878-XiMat	blood
22	chr1:9649800-9652400	Enhancers	Lung	lung
23	chr1:9649800-9654400	Enhancers	Spleen	Spleen
24	chr1:9649800-9657200	Enhancers	Fetal Heart	heart
25	chr1:9649800-9657400	Enhancers	Placenta	Placenta
26	chr1:9649800-9657400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr1:9650000-9650800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:9650000-9650800	Enhancers	Thymus	Thymus
29	chr1:9650000-9651000	Enhancers	Gastric	stomach
30	chr1:9650000-9651200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
31	chr1:9650000-9651600	Enhancers	Fetal Lung	lung
32	chr1:9650000-9651800	Transcr. at gene 5' and 3'	Dnd41	blood
33	chr1:9650000-9652600	Genic enhancers	Fetal Stomach	stomach
34	chr1:9650000-9653200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr1:9650000-9653200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr1:9650000-9653200	Weak transcription	Small Intestine	intestine
37	chr1:9650000-9654000	Enhancers	HSMMtube	muscle
38	chr1:9650000-9654200	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr1:9650000-9654200	Enhancers	Primary B cells from cord blood	blood
40	chr1:9650000-9654200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:9650000-9654200	Enhancers	Left Ventricle	heart
42	chr1:9650000-9654400	Enhancers	Right Atrium	heart
43	chr1:9650000-9655400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:9650000-9656000	Enhancers	Psoas Muscle	Psoas
45	chr1:9650000-9661200	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr1:9650200-9650800	Enhancers	Primary T cells fromperipheralblood	blood
47	chr1:9650200-9650800	Enhancers	Fetal Thymus	thymus
48	chr1:9650200-9651000	Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr1:9650200-9651000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:9650200-9651000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood

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