Variant report

Variant	rs1203427
Chromosome Location	chr10:52191781-52191782
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:52191418..52195182-chr10:52381701..52384353,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198964	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1203374	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203379	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203380	0.83[TSI][hapmap]
rs1203383	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203384	1.00[CEU][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203391	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203402	0.90[CEU][hapmap];0.86[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1203412	1.00[CEU][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]
rs1203416	1.00[ASN][1000 genomes]
rs1203417	1.00[ASN][1000 genomes]
rs1203419	1.00[ASN][1000 genomes]
rs1203422	1.00[ASN][1000 genomes]
rs1203426	0.82[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1209146	0.98[EUR][1000 genomes]
rs1211373	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1212555	0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs2024871	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2064760	0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs2208035	0.91[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2474611	1.00[ASN][1000 genomes]
rs2574945	1.00[ASN][1000 genomes]
rs2574976	0.93[GIH][hapmap];1.00[ASN][1000 genomes]
rs2688874	1.00[ASN][1000 genomes]
rs2688876	1.00[ASN][1000 genomes]
rs2688883	1.00[ASN][1000 genomes]
rs2688884	0.93[GIH][hapmap];1.00[ASN][1000 genomes]
rs2842099	1.00[ASN][1000 genomes]
rs2842110	1.00[GIH][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs2860490	0.85[TSI][hapmap]
rs2983346	0.80[EUR][1000 genomes]
rs2983348	0.91[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2983349	0.80[EUR][1000 genomes]
rs2983352	0.82[TSI][hapmap]
rs2983362	0.88[MEX][hapmap];0.85[TSI][hapmap]
rs2983363	0.85[TSI][hapmap]
rs2983372	0.91[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011711	0.85[TSI][hapmap]
rs3011712	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011715	1.00[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011768	0.89[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011795	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7094723	0.80[CEU][hapmap]
rs72801753	1.00[ASN][1000 genomes]
rs7923756	1.00[GIH][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs910818	0.80[EUR][1000 genomes]
rs910819	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9416590	1.00[CEU][hapmap];0.90[EUR][1000 genomes];1.00[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
rs1203427	CSTF2T	cis	parietal	SCAN
rs1203427	C10orf71	cis	parietal	SCAN
rs1203427	A1CF	cis	parietal	SCAN

Chromatin state (count:80 , 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	chr10:52179200-52196600	Weak transcription	Colon Smooth Muscle	Colon
10	chr10:52180200-52201200	Weak transcription	Fetal Heart	heart
11	chr10:52180600-52194000	Weak transcription	Fetal Intestine Large	intestine
12	chr10:52181600-52219400	Weak transcription	Placenta	Placenta
13	chr10:52181800-52206200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr10:52182200-52220000	Weak transcription	Fetal Stomach	stomach
15	chr10:52182600-52200600	Weak transcription	Fetal Brain Male	brain
16	chr10:52188600-52192200	Weak transcription	K562	blood
17	chr10:52189800-52192400	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr10:52189800-52194400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr10:52190400-52192400	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr10:52190600-52191800	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr10:52190800-52192000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr10:52190800-52192200	Enhancers	Pancreatic Islets	Pancreatic Islet
23	chr10:52190800-52192400	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr10:52190800-52192600	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr10:52191000-52191800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr10:52191000-52191800	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr10:52191000-52191800	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr10:52191000-52191800	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr10:52191000-52191800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr10:52191000-52191800	Enhancers	Fetal Lung	lung
31	chr10:52191000-52191800	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr10:52191000-52191800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr10:52191000-52191800	Enhancers	NH-A	brain
34	chr10:52191000-52192000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr10:52191000-52192000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr10:52191000-52192000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr10:52191000-52193000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr10:52191000-52193000	Flanking Active TSS	GM12878-XiMat	blood
39	chr10:52191000-52193400	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr10:52191000-52193800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr10:52191200-52191800	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr10:52191200-52191800	Enhancers	Primary B cells from peripheral blood	blood
43	chr10:52191200-52191800	Enhancers	Liver	Liver
44	chr10:52191200-52191800	Flanking Active TSS	Brain Anterior Caudate	brain
45	chr10:52191200-52191800	Flanking Active TSS	Hela-S3	cervix
46	chr10:52191200-52191800	Flanking Active TSS	Osteobl	bone
47	chr10:52191200-52192000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr10:52191200-52192000	Enhancers	Brain Angular Gyrus	brain
49	chr10:52191200-52192000	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr10:52191200-52192400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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