Variant report

Variant	rs1590445
Chromosome Location	chr10:27071250-27071251
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:27064202..27066612-chr10:27068536..27071634,3	K562	blood:
2	chr10:27063322..27065877-chr10:27068617..27071382,2	K562	blood:
3	chr10:27070974..27073894-chr10:27148134..27150716,3	MCF-7	breast:
4	chr10:27054901..27057514-chr10:27069095..27071711,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136754	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1031858	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10741117	0.87[CEU][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10741119	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10741121	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10764638	0.92[CEU][hapmap];0.94[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10764639	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10764641	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10764643	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10829063	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10829064	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10829071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12221102	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1324637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1409130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1542553	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1543849	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1998631	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1998632	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1998634	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2031562	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2148110	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2182293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2368184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2368185	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3802612	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3916988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4376804	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4747575	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4749185	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6482575	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7078119	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7078227	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7895417	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7895559	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7907630	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7915128	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	esv3415799	chr10:26929831-27233591	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv933544	chr10:27005220-27111998	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv831812	chr10:27061506-27234267	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv971858	chr10:27066006-27157708	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv6132	chr10:27066081-27075522	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1590445	MYO3A	cis	cerebellum	SCAN
rs1590445	LYZL2	cis	cerebellum	SCAN
rs1590445	WAC	cis	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:27044800-27082000	Weak transcription	Fetal Lung	lung
2	chr10:27051400-27082000	Weak transcription	Fetal Stomach	stomach
3	chr10:27057800-27072000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr10:27058000-27072200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr10:27058000-27079200	Weak transcription	Dnd41	blood
6	chr10:27064600-27074200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr10:27066200-27074600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr10:27066400-27074000	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr10:27066400-27074600	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr10:27066400-27075200	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr10:27066800-27073400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr10:27067200-27073000	Enhancers	Primary B cells from peripheral blood	blood
13	chr10:27067600-27072200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr10:27067800-27071400	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr10:27068200-27072000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr10:27068400-27071800	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr10:27068400-27072000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr10:27068400-27079400	Weak transcription	Primary hematopoietic stem cells	blood
19	chr10:27068600-27073000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr10:27068600-27074200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr10:27069000-27071600	Enhancers	Primary T cells fromperipheralblood	blood
22	chr10:27069000-27072400	Weak transcription	HepG2	liver
23	chr10:27069000-27073000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr10:27069200-27078800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr10:27069400-27071400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr10:27069400-27071400	Enhancers	Brain Anterior Caudate	brain
27	chr10:27069400-27073000	Enhancers	Small Intestine	intestine
28	chr10:27069400-27079600	Weak transcription	K562	blood
29	chr10:27069600-27071400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr10:27069600-27071400	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr10:27069800-27071400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr10:27069800-27075000	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr10:27069800-27084600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr10:27070000-27074000	Enhancers	Brain Substantia Nigra	brain
35	chr10:27070200-27071400	Enhancers	Fetal Heart	heart
36	chr10:27070200-27076600	Weak transcription	Fetal Muscle Leg	muscle
37	chr10:27070400-27071800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr10:27070600-27071400	Enhancers	NH-A	brain
39	chr10:27070600-27071800	Enhancers	Hela-S3	cervix
40	chr10:27070600-27072800	Weak transcription	Fetal Thymus	thymus
41	chr10:27070600-27073000	Weak transcription	Colon Smooth Muscle	Colon
42	chr10:27070600-27074400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr10:27070600-27082800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr10:27070800-27072200	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr10:27070800-27091800	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr10:27071000-27071400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr10:27071000-27071800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr10:27071000-27072000	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr10:27071000-27072000	Enhancers	GM12878-XiMat	blood
50	chr10:27071000-27072200	Enhancers	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links