Variant report

Variant	rs1203410
Chromosome Location	chr10:52196945-52196946
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:52193457..52195166-chr10:52196882..52200363,3	K562	blood:
2	chr10:52194860..52197104-chr10:52213485..52214996,2	K562	blood:
3	chr10:52185055..52188816-chr10:52196257..52198755,3	MCF-7	breast:
4	chr10:52182601..52184931-chr10:52195030..52197697,2	K562	blood:

Extended variants
information (count: 86 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10508931	0.86[CHB][hapmap]
rs11005626	0.85[YRI][hapmap]
rs11005832	0.95[YRI][hapmap]
rs11006190	0.86[CHB][hapmap]
rs11006191	0.86[CHB][hapmap]
rs11006193	0.86[CHB][hapmap]
rs11006194	1.00[CHB][hapmap]
rs11006197	0.86[CHB][hapmap]
rs11006200	0.86[CHB][hapmap]
rs11006213	0.86[CHB][hapmap]
rs11006233	0.86[CHB][hapmap]
rs11006237	0.86[CHB][hapmap]
rs11006238	0.86[CHB][hapmap]
rs1203375	1.00[CHD][hapmap];0.82[MEX][hapmap];0.90[YRI][hapmap];0.90[ASN][1000 genomes]
rs1203382	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1203386	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1203390	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1203393	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1203394	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203395	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203401	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1203403	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203405	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203407	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203411	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203413	0.85[TSI][hapmap]
rs1203418	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1203420	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1203421	0.81[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12246361	0.95[YRI][hapmap]
rs12257419	0.83[YRI][hapmap]
rs12260887	0.85[YRI][hapmap]
rs12264511	0.85[YRI][hapmap]
rs12264817	0.95[YRI][hapmap]
rs12267134	0.84[YRI][hapmap]
rs1740761	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17496403	0.86[CHB][hapmap]
rs17496500	0.86[CHB][hapmap]
rs1810576	0.93[ASN][1000 genomes]
rs1916567	0.81[CEU][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2221	0.95[CEU][hapmap];0.86[CHB][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2339402	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2574985	0.95[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.92[ASN][1000 genomes]
rs2842103	0.81[TSI][hapmap]
rs2983347	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2983350	0.94[CEU][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs2983354	1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2983357	0.95[CEU][hapmap];0.86[CHB][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2983359	0.95[CEU][hapmap];0.86[CHB][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2983361	0.95[CEU][hapmap];0.86[CHB][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2983368	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2983369	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2983370	0.84[ASN][1000 genomes]
rs2983371	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3011770	0.90[CEU][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes]
rs3011771	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3011773	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3011779	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3011780	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3011782	0.90[CEU][hapmap];0.86[CHB][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3011783	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3011786	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3011787	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3011788	0.95[CEU][hapmap];0.86[CHB][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3011789	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3011790	0.95[CEU][hapmap];0.86[CHB][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3011791	0.95[CEU][hapmap];0.86[CHB][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3011792	0.95[CEU][hapmap];0.86[CHB][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3011793	0.84[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs3011794	0.95[CEU][hapmap];0.86[CHB][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.83[ASN][1000 genomes]
rs3011797	0.95[CEU][hapmap];0.86[CHB][hapmap];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3011801	0.95[CEU][hapmap];0.86[CHB][hapmap];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4312019	0.81[TSI][hapmap]
rs7068377	0.90[YRI][hapmap]
rs7072826	0.86[CHB][hapmap]
rs7912351	0.83[ASN][1000 genomes]
rs7921226	0.86[CHB][hapmap]
rs920136	0.91[ASW][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.90[YRI][hapmap];0.92[ASN][1000 genomes]
rs9988708	0.90[ASW][hapmap];1.00[YRI][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	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv521273	chr10:52051645-52197847	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1203410	PARG	cis	parietal	SCAN
rs1203410	MSMB	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52178400-52220000	Weak transcription	Pancreas	Pancrea
2	chr10:52178600-52217200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr10:52178600-52219400	Weak transcription	Left Ventricle	heart
4	chr10:52178800-52198000	Weak transcription	Fetal Thymus	thymus
5	chr10:52178800-52202800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr10:52179000-52205800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr10:52179000-52207600	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr10:52179000-52209000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr10:52180200-52201200	Weak transcription	Fetal Heart	heart
10	chr10:52181600-52219400	Weak transcription	Placenta	Placenta
11	chr10:52181800-52206200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr10:52182200-52220000	Weak transcription	Fetal Stomach	stomach
13	chr10:52182600-52200600	Weak transcription	Fetal Brain Male	brain
14	chr10:52191400-52200400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr10:52191600-52207600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr10:52191600-52211200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr10:52191800-52197000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr10:52191800-52205400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr10:52191800-52219600	Weak transcription	Fetal Lung	lung
20	chr10:52192000-52219600	Weak transcription	Adipose Nuclei	Adipose
21	chr10:52192200-52197000	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr10:52192400-52197000	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr10:52192400-52198200	Weak transcription	Right Atrium	heart
24	chr10:52192400-52199400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr10:52192400-52199600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr10:52192400-52200800	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr10:52192400-52202600	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr10:52192400-52207600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr10:52192400-52219400	Weak transcription	Liver	Liver
30	chr10:52192400-52219600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr10:52192400-52219600	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr10:52192400-52220000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr10:52192400-52229400	Weak transcription	Aorta	Aorta
34	chr10:52192400-52230400	Weak transcription	HSMM	muscle
35	chr10:52193000-52197400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr10:52193000-52207400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr10:52193400-52205400	Weak transcription	Primary B cells from cord blood	blood
38	chr10:52193400-52206200	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr10:52193800-52198200	Weak transcription	K562	blood
40	chr10:52194000-52197000	Weak transcription	HSMMtube	muscle
41	chr10:52194000-52197200	Weak transcription	GM12878-XiMat	blood
42	chr10:52194200-52207600	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr10:52194400-52197200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr10:52195200-52198000	Weak transcription	Primary B cells from peripheral blood	blood
45	chr10:52195800-52197600	Weak transcription	Spleen	Spleen
46	chr10:52196200-52197600	Enhancers	Brain Angular Gyrus	brain
47	chr10:52196200-52197800	Enhancers	Brain Substantia Nigra	brain
48	chr10:52196200-52198000	Enhancers	Brain Cingulate Gyrus	brain
49	chr10:52196200-52198200	Enhancers	Brain Hippocampus Middle	brain
50	chr10:52196200-52198800	Strong transcription	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links