Variant report

Variant	rs1572860
Chromosome Location	chr10:99310982-99310983
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:99258572..99260331-chr10:99308724..99311083,3	MCF-7	breast:
2	chr10:99299652..99304961-chr10:99307189..99311108,10	MCF-7	breast:
3	chr10:99307089..99309387-chr10:99309451..99312013,2	MCF-7	breast:
4	chr10:99296840..99298523-chr10:99309435..99312063,2	MCF-7	breast:
5	chr10:99303622..99306407-chr10:99309864..99312001,2	K562	blood:

Variant related genes	Relation type
ENSG00000165886	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10748698	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10748699	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10748700	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882956	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10882957	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10882959	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10882961	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882962	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10882963	1.00[CEU][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes]
rs10882965	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10882966	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1107517	0.80[EUR][1000 genomes]
rs1107518	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11189244	0.88[MEX][hapmap]
rs11189245	0.82[MEX][hapmap]
rs11189253	0.82[CHB][hapmap]
rs11189259	0.82[MEX][hapmap]
rs11189266	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11189270	0.84[EUR][1000 genomes]
rs11189274	0.95[CEU][hapmap];0.87[GIH][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs11189275	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11189278	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11189281	0.87[CHB][hapmap];0.80[JPT][hapmap]
rs11189284	0.90[CEU][hapmap]
rs11511362	0.86[EUR][1000 genomes]
rs11528108	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11528109	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11814566	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs12219064	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12221474	0.93[ASW][hapmap];0.94[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12243136	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12415338	0.84[EUR][1000 genomes]
rs12766074	0.85[EUR][1000 genomes]
rs12774288	0.80[EUR][1000 genomes]
rs12775868	0.81[EUR][1000 genomes]
rs12783481	0.83[EUR][1000 genomes]
rs1417408	0.95[CEU][hapmap];0.87[GIH][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs1475757	0.80[ASN][1000 genomes]
rs17108059	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2282373	0.80[CEU][hapmap]
rs3814554	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs3818910	0.90[CEU][hapmap]
rs4635019	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4919104	0.86[CHB][hapmap];0.81[JPT][hapmap];0.88[MEX][hapmap]
rs4919108	0.85[EUR][1000 genomes]
rs4919109	0.81[EUR][1000 genomes]
rs7077211	0.95[ASN][1000 genomes]
rs7077976	0.86[EUR][1000 genomes]
rs7089060	0.83[CHB][hapmap]
rs7094973	0.85[CEU][hapmap]
rs7342022	0.87[EUR][1000 genomes]
rs7475470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7475851	0.84[EUR][1000 genomes]
rs7893335	0.88[MEX][hapmap]
rs7902642	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7921278	0.89[ASN][1000 genomes]
rs7921505	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1817777	chr10:99196035-99558169	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1036494	chr10:99267639-99345207	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	nsv7508	chr10:99285375-99330501	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	nsv1047359	chr10:99306501-99369013	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1572860	C10orf28	cis	cerebellum	SCAN
rs1572860	WNT8B	cis	cerebellum	SCAN
rs1572860	HOGA1	cis	lymphoblastoid	seeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99303000-99327600	Weak transcription	Aorta	Aorta
2	chr10:99303200-99327600	Weak transcription	Pancreas	Pancrea
3	chr10:99303800-99327800	Weak transcription	Ovary	ovary
4	chr10:99304200-99313400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr10:99306000-99311000	Enhancers	Fetal Muscle Leg	muscle
6	chr10:99306400-99311000	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr10:99306400-99311200	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr10:99306400-99311400	Enhancers	Psoas Muscle	Psoas
9	chr10:99306600-99311400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr10:99307000-99311400	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr10:99307200-99313600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr10:99307600-99311400	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr10:99307600-99311400	Enhancers	HMEC	breast
14	chr10:99308000-99313200	Weak transcription	HUVEC	blood vessel
15	chr10:99308200-99313200	Weak transcription	NHLF	lung
16	chr10:99308600-99311000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr10:99308600-99311400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr10:99308600-99311400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr10:99308600-99311600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr10:99308600-99311800	Enhancers	Placenta Amnion	Placenta Amnion
21	chr10:99308800-99311000	Enhancers	Placenta	Placenta
22	chr10:99308800-99311400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr10:99308800-99311400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr10:99309000-99311000	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr10:99309200-99311400	Enhancers	H1 Cell Line	embryonic stem cell
26	chr10:99309400-99313200	Weak transcription	A549	lung
27	chr10:99309600-99311000	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr10:99309600-99313200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr10:99309800-99313000	Weak transcription	Stomach Smooth Muscle	stomach
30	chr10:99309800-99313400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr10:99309800-99316200	Weak transcription	Liver	Liver
32	chr10:99310000-99311000	Enhancers	Fetal Kidney	kidney
33	chr10:99310000-99311600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr10:99310000-99313200	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr10:99310000-99313200	Weak transcription	Adipose Nuclei	Adipose
36	chr10:99310000-99313200	Weak transcription	Fetal Stomach	stomach
37	chr10:99310000-99313200	Weak transcription	NH-A	brain
38	chr10:99310200-99313200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr10:99310200-99313400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr10:99310400-99311400	Enhancers	K562	blood
41	chr10:99310400-99311800	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr10:99310400-99312200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr10:99310400-99327600	Weak transcription	Lung	lung
44	chr10:99310400-99327800	Weak transcription	Right Ventricle	heart
45	chr10:99310600-99311000	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr10:99310600-99311600	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr10:99310600-99313000	Weak transcription	Fetal Muscle Trunk	muscle
48	chr10:99310600-99313200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr10:99310600-99313200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr10:99310600-99313200	Weak transcription	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links