Variant report

Variant	rs749966
Chromosome Location	chr1:154314408-154314409
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	chr1:154303313..154308700-chr1:154311319..154315527,5	MCF-7	breast:
2	chr1:154307733..154310042-chr1:154313433..154315185,2	K562	blood:

Variant related genes	Relation type
ENSG00000143515	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs11265594	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11809740	0.82[CHD][hapmap];0.87[GIH][hapmap]
rs12058332	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12063437	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12066892	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12068128	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12729561	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12749618	0.94[EUR][1000 genomes]
rs16865579	0.91[EUR][1000 genomes]
rs1760796	0.86[JPT][hapmap]
rs1889316	0.91[EUR][1000 genomes]
rs1931299	0.82[ASN][1000 genomes]
rs1948143	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2297607	0.87[CHD][hapmap];0.81[GIH][hapmap]
rs28410194	0.91[EUR][1000 genomes]
rs28530583	0.91[EUR][1000 genomes]
rs2988721	0.87[CHD][hapmap];0.91[GIH][hapmap]
rs34065906	0.82[EUR][1000 genomes]
rs34146123	0.82[EUR][1000 genomes]
rs34640592	0.89[ASN][1000 genomes]
rs34749203	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34880256	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34968830	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35091500	0.88[EUR][1000 genomes]
rs35112510	0.90[EUR][1000 genomes]
rs35229198	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35362987	0.89[ASN][1000 genomes]
rs35387092	0.84[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.89[MKK][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs35595831	0.81[EUR][1000 genomes]
rs35629421	0.91[EUR][1000 genomes]
rs35800693	0.89[ASN][1000 genomes]
rs36029470	0.84[EUR][1000 genomes]
rs3811451	0.91[EUR][1000 genomes]
rs3811452	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3916566	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.90[MKK][hapmap];0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4304577	0.91[EUR][1000 genomes]
rs4406622	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4414034	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4622059	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56023096	0.94[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs56367957	0.89[ASN][1000 genomes]
rs61578738	0.87[ASN][1000 genomes]
rs61803412	0.91[EUR][1000 genomes]
rs61803414	0.91[EUR][1000 genomes]
rs61804488	0.82[EUR][1000 genomes]
rs61804489	0.82[EUR][1000 genomes]
rs61812565	0.81[EUR][1000 genomes]
rs6427560	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6427561	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6662855	0.91[EUR][1000 genomes]
rs6662976	0.93[EUR][1000 genomes]
rs6663105	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6667225	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6672627	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6686621	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6690468	0.91[EUR][1000 genomes]
rs6701309	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs68031662	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs68138282	0.81[EUR][1000 genomes]
rs7511806	0.87[EUR][1000 genomes]
rs7518394	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7523399	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7530735	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7530868	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7547298	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7552370	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9728024	0.86[EUR][1000 genomes]
rs9787014	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
4	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
5	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
6	esv3451054	chr1:154182013-154360141	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
7	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs749966	DCST1	cis	parietal	SCAN
rs749966	C1orf43	cis	cerebellum	SCAN
rs749966	SYT11	cis	cerebellum	SCAN
rs749966	CKS1B	cis	cerebellum	SCAN
rs749966	GATAD2B	cis	parietal	SCAN
rs749966	S100A14	cis	cerebellum	SCAN
rs749966	RORC	cis	cerebellum	SCAN
rs749966	SCAMP3	cis	parietal	SCAN
rs749966	HAX1	cis	cerebellum	SCAN
rs749966	S100A8	cis	parietal	SCAN
rs749966	SHC1	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154301400-154318400	Weak transcription	Small Intestine	intestine
2	chr1:154302200-154322400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:154302400-154322400	Strong transcription	Dnd41	blood
4	chr1:154302400-154323200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:154302600-154318200	Weak transcription	Fetal Heart	heart
6	chr1:154302600-154320800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:154302600-154322600	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr1:154302600-154323000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:154302800-154323000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:154303000-154322200	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr1:154303000-154322600	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr1:154303200-154322200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr1:154303200-154322400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:154303200-154323400	Strong transcription	Fetal Brain Female	brain
15	chr1:154303200-154324600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr1:154304000-154322000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:154304800-154317800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr1:154305800-154322200	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr1:154306400-154322400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
20	chr1:154307200-154314600	Weak transcription	NHEK	skin
21	chr1:154307600-154314800	Strong transcription	HSMMtube	muscle
22	chr1:154307600-154322600	Strong transcription	Osteobl	bone
23	chr1:154307600-154324600	Weak transcription	Right Atrium	heart
24	chr1:154307800-154316400	Weak transcription	Liver	Liver
25	chr1:154307800-154323200	Strong transcription	Fetal Stomach	stomach
26	chr1:154307800-154323200	Strong transcription	NHLF	lung
27	chr1:154308000-154314600	Strong transcription	Muscle Satellite Cultured Cells	--
28	chr1:154308000-154321000	Weak transcription	Stomach Mucosa	stomach
29	chr1:154308000-154322600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:154308000-154323000	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr1:154308200-154314600	Strong transcription	Fetal Muscle Trunk	muscle
32	chr1:154308200-154320600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:154308200-154322200	Strong transcription	Fetal Muscle Leg	muscle
34	chr1:154308200-154323000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:154308200-154323200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:154308200-154323400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:154308600-154323000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr1:154309400-154322400	Strong transcription	Brain Cingulate Gyrus	brain
39	chr1:154309400-154322400	Strong transcription	NHDF-Ad	bronchial
40	chr1:154309600-154314800	Strong transcription	Primary B cells from peripheral blood	blood
41	chr1:154309600-154314800	Strong transcription	Adipose Nuclei	Adipose
42	chr1:154309600-154319200	Strong transcription	Aorta	Aorta
43	chr1:154309600-154319400	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr1:154309600-154319600	Strong transcription	NH-A	brain
45	chr1:154309600-154321800	Strong transcription	Fetal Lung	lung
46	chr1:154309600-154322200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:154309600-154322400	Strong transcription	Left Ventricle	heart
48	chr1:154309600-154322400	Strong transcription	Thymus	Thymus
49	chr1:154309600-154322800	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr1:154309600-154323000	Strong transcription	Brain Germinal Matrix	brain

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