Variant report

Variant	rs1203408
Chromosome Location	chr10:52197398-52197399
allele	A/G
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	chr10:52185055..52188816-chr10:52196257..52198755,3	MCF-7	breast:
3	chr10:52182601..52184931-chr10:52195030..52197697,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1203381	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1203387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1203388	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1203389	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1203392	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1203396	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203398	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203399	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203400	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1203404	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1203406	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1210065	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1210066	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1211496	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1212555	0.93[YRI][hapmap]
rs1740759	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2461912	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7099450	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7893281	0.98[ASN][1000 genomes]
rs927046	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1203408	CSTF2T	cis	parietal	SCAN
rs1203408	MSMB	cis	parietal	SCAN
rs1203408	PARG	cis	parietal	SCAN

Chromatin state (count:56 , 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	chr10:52191800-52205400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr10:52191800-52219600	Weak transcription	Fetal Lung	lung
19	chr10:52192000-52219600	Weak transcription	Adipose Nuclei	Adipose
20	chr10:52192400-52198200	Weak transcription	Right Atrium	heart
21	chr10:52192400-52199400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr10:52192400-52199600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr10:52192400-52200800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr10:52192400-52202600	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr10:52192400-52207600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr10:52192400-52219400	Weak transcription	Liver	Liver
27	chr10:52192400-52219600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr10:52192400-52219600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr10:52192400-52220000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr10:52192400-52229400	Weak transcription	Aorta	Aorta
31	chr10:52192400-52230400	Weak transcription	HSMM	muscle
32	chr10:52193000-52197400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr10:52193000-52207400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr10:52193400-52205400	Weak transcription	Primary B cells from cord blood	blood
35	chr10:52193400-52206200	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr10:52193800-52198200	Weak transcription	K562	blood
37	chr10:52194200-52207600	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr10:52195200-52198000	Weak transcription	Primary B cells from peripheral blood	blood
39	chr10:52195800-52197600	Weak transcription	Spleen	Spleen
40	chr10:52196200-52197600	Enhancers	Brain Angular Gyrus	brain
41	chr10:52196200-52197800	Enhancers	Brain Substantia Nigra	brain
42	chr10:52196200-52198000	Enhancers	Brain Cingulate Gyrus	brain
43	chr10:52196200-52198200	Enhancers	Brain Hippocampus Middle	brain
44	chr10:52196200-52198800	Strong transcription	Primary T cells from cord blood	blood
45	chr10:52196400-52198800	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr10:52196600-52197800	Enhancers	Colon Smooth Muscle	Colon
47	chr10:52196800-52197600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
48	chr10:52196800-52199200	Enhancers	Brain Anterior Caudate	brain
49	chr10:52197000-52198000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr10:52197000-52199200	Enhancers	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links