Variant report

Variant	rs1061122
Chromosome Location	chr1:154832290-154832291
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10908443	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11264302	1.00[JPT][hapmap]
rs11264303	1.00[JPT][hapmap]
rs11582128	1.00[JPT][hapmap]
rs1218554	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1218584	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1218585	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1218587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1218588	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1218589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1218592	1.00[ASN][1000 genomes]
rs12760148	1.00[CHB][hapmap]
rs16836525	1.00[CHB][hapmap]
rs2878412	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4845396	1.00[CHB][hapmap]
rs4845397	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4845402	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4845675	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6660884	1.00[JPT][hapmap]
rs6682335	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs906596	0.84[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs906597	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer 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	575 gene(s)	inside rSNPs	diseases
2	nsv427797	chr1:154559115-154933717	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv432931	chr1:154794318-154855055	Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	esv29982	chr1:154818353-154882544	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv432942	chr1:154818353-154903047	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv432964	chr1:154820067-154849590	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv432953	chr1:154820067-154855055	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1061122	S100A7L2	cis	parietal	SCAN
rs1061122	PSMD4	cis	cerebellum	SCAN
rs1061122	C1orf85	cis	parietal	SCAN
rs1061122	LENEP	cis	cerebellum	SCAN
rs1061122	BCAN	cis	parietal	SCAN
rs1061122	INTS3	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154820800-154832600	Weak transcription	Right Atrium	heart
2	chr1:154821000-154837200	Weak transcription	Colon Smooth Muscle	Colon
3	chr1:154822600-154838000	Weak transcription	Brain Angular Gyrus	brain
4	chr1:154823400-154832400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:154824400-154834200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:154827600-154839400	Enhancers	Fetal Brain Male	brain
7	chr1:154827800-154833600	Enhancers	Fetal Muscle Leg	muscle
8	chr1:154828000-154833400	Enhancers	Brain Anterior Caudate	brain
9	chr1:154828400-154833400	Flanking Active TSS	GM12878-XiMat	blood
10	chr1:154828800-154832600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:154829000-154832600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:154829200-154833000	Weak transcription	Brain Substantia Nigra	brain
13	chr1:154829400-154832400	Weak transcription	Brain Hippocampus Middle	brain
14	chr1:154830400-154832800	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr1:154830600-154832400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:154830600-154833400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
17	chr1:154830800-154832600	Weak transcription	NH-A	brain
18	chr1:154830800-154834000	Strong transcription	Fetal Stomach	stomach
19	chr1:154831200-154839800	Enhancers	Psoas Muscle	Psoas
20	chr1:154831400-154832400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
21	chr1:154831400-154839400	Enhancers	Primary B cells from peripheral blood	blood
22	chr1:154831600-154832800	Active TSS	Duodenum Mucosa	Duodenum
23	chr1:154831600-154833000	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr1:154831600-154833400	Enhancers	Brain Germinal Matrix	brain
25	chr1:154831600-154835200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:154831800-154832600	Enhancers	Monocytes-CD14+_RO01746	blood
27	chr1:154831800-154832800	Enhancers	Brain Cingulate Gyrus	brain
28	chr1:154831800-154833400	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr1:154831800-154833400	Enhancers	Right Ventricle	heart
30	chr1:154831800-154835800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
31	chr1:154831800-154839400	Enhancers	Fetal Thymus	thymus
32	chr1:154832000-154832400	Enhancers	HSMMtube	muscle
33	chr1:154832000-154833000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:154832000-154833000	Enhancers	Spleen	Spleen
35	chr1:154832000-154833200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr1:154832000-154833200	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr1:154832000-154834400	Enhancers	Thymus	Thymus
38	chr1:154832000-154834800	Enhancers	Primary B cells from cord blood	blood
39	chr1:154832000-154837000	Enhancers	HSMM	muscle
40	chr1:154832200-154832400	Enhancers	Stomach Smooth Muscle	stomach
41	chr1:154832200-154832600	Active TSS	Fetal Brain Female	brain
42	chr1:154832200-154832800	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr1:154832200-154832800	Weak transcription	Colonic Mucosa	Colon
44	chr1:154832200-154832800	Enhancers	HMEC	breast
45	chr1:154832200-154833000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr1:154832200-154834200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:154832200-154836600	Enhancers	Muscle Satellite Cultured Cells	--

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