Variant report

Variant	rs2025544
Chromosome Location	chr9:115632969-115632970
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	chr9:115632762..115634297-chr9:115636411..115638284,2	K562	blood:

Extended variants
information (count: 113 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10115576	1.00[CEU][hapmap];0.88[GIH][hapmap]
rs10115711	0.82[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10124260	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs10124939	0.82[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs10124979	0.82[CEU][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10733594	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs10733598	1.00[CEU][hapmap];0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs10733599	1.00[CEU][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739370	0.82[CEU][hapmap];1.00[ASN][1000 genomes]
rs10739373	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs10739374	1.00[ASN][1000 genomes]
rs10739376	1.00[CEU][hapmap];0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs10739378	1.00[CEU][hapmap]
rs10739380	0.83[EUR][1000 genomes]
rs10759590	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs10759603	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs10759604	1.00[ASN][1000 genomes]
rs1158331	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1324931	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs1361720	0.85[CEU][hapmap]
rs1418409	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs1475293	1.00[CEU][hapmap];0.88[GIH][hapmap]
rs1539338	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs1570754	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1693411	1.00[ASN][1000 genomes]
rs1711746	1.00[ASN][1000 genomes]
rs1711747	0.86[GIH][hapmap];1.00[ASN][1000 genomes]
rs1832890	1.00[ASN][1000 genomes]
rs1891402	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs1891403	0.85[CEU][hapmap];0.88[GIH][hapmap]
rs2051018	1.00[ASN][1000 genomes]
rs2147643	1.00[ASN][1000 genomes]
rs2147646	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2153837	0.81[GIH][hapmap];1.00[ASN][1000 genomes]
rs2182048	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2185769	1.00[ASN][1000 genomes]
rs2645985	1.00[ASN][1000 genomes]
rs2645993	0.85[CEU][hapmap]
rs2645994	0.87[GIH][hapmap];1.00[ASN][1000 genomes]
rs2796025	1.00[ASN][1000 genomes]
rs2796028	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs2796031	1.00[ASN][1000 genomes]
rs2796035	1.00[ASN][1000 genomes]
rs4246892	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs4304397	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap]
rs4360356	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4549852	1.00[ASN][1000 genomes]
rs4978507	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs4978510	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4978511	0.82[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs4979153	0.85[CEU][hapmap]
rs4979154	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs4979155	1.00[ASN][1000 genomes]
rs4979157	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs4979165	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs4979170	1.00[CEU][hapmap]
rs4979171	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4979183	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4979184	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4979186	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6477959	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs700122	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs7026450	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7030795	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs7038684	1.00[ASN][1000 genomes]
rs7040954	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7041965	1.00[ASN][1000 genomes]
rs7047914	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7859175	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs7868830	0.85[CEU][hapmap]
rs7869100	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs786961	1.00[ASW][hapmap];0.87[GIH][hapmap];1.00[ASN][1000 genomes]
rs786965	1.00[ASN][1000 genomes]
rs786966	0.87[GIH][hapmap];1.00[ASN][1000 genomes]
rs786967	1.00[ASN][1000 genomes]
rs786968	0.87[GIH][hapmap];1.00[ASN][1000 genomes]
rs786969	1.00[ASN][1000 genomes]
rs786972	1.00[ASN][1000 genomes]
rs786973	1.00[ASN][1000 genomes]
rs786977	0.87[GIH][hapmap];1.00[ASN][1000 genomes]
rs7872628	1.00[ASN][1000 genomes]
rs787271	0.85[CEU][hapmap];0.88[GIH][hapmap]
rs787274	0.88[GIH][hapmap]
rs787276	0.85[CEU][hapmap]
rs787278	1.00[ASN][1000 genomes]
rs787280	0.85[CEU][hapmap];0.88[GIH][hapmap]
rs787281	1.00[ASN][1000 genomes]
rs787284	0.85[CEU][hapmap]
rs787285	1.00[ASN][1000 genomes]
rs787286	1.00[ASN][1000 genomes]
rs787287	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs787291	1.00[ASN][1000 genomes]
rs787294	0.85[CEU][hapmap]
rs787295	0.85[CEU][hapmap];0.88[GIH][hapmap]
rs787296	1.00[ASN][1000 genomes]
rs787297	0.85[CEU][hapmap];0.88[GIH][hapmap]
rs787298	0.85[CEU][hapmap]
rs787299	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs787301	0.85[CEU][hapmap];0.87[GIH][hapmap]
rs787302	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs787303	1.00[ASN][1000 genomes]
rs7873289	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs813101	0.85[CEU][hapmap]
rs885387	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs912662	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9409123	0.85[CEU][hapmap]
rs947609	1.00[ASN][1000 genomes]
rs980345	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	esv2758198	chr9:115240454-116002951	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription 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	57 gene(s)	inside rSNPs	diseases
2	esv2759710	chr9:115240454-116002951	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv893733	chr9:115397206-115712068	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers 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	24 gene(s)	inside rSNPs	diseases
4	esv2422302	chr9:115550339-115656433	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv1047000	chr9:115610445-115884038	ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2025544	TSCOT	cis	multi-tissue	Pritchard

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115594200-115634400	Weak transcription	NH-A	brain
2	chr9:115601200-115641200	Weak transcription	Fetal Brain Male	brain
3	chr9:115607400-115643400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr9:115611400-115634600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:115611600-115634200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr9:115612000-115634600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr9:115613600-115642600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr9:115615600-115639200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:115615600-115646400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr9:115621200-115639400	Weak transcription	Stomach Mucosa	stomach
11	chr9:115624200-115652600	Weak transcription	Fetal Heart	heart
12	chr9:115624800-115635200	Strong transcription	Primary T cells from cord blood	blood
13	chr9:115625600-115633400	Weak transcription	Right Atrium	heart
14	chr9:115625800-115645200	Weak transcription	Thymus	Thymus
15	chr9:115626000-115636200	Weak transcription	NHLF	lung
16	chr9:115626400-115634200	Strong transcription	Stomach Smooth Muscle	stomach
17	chr9:115626400-115635000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr9:115626400-115635200	Strong transcription	Fetal Stomach	stomach
19	chr9:115626400-115650800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr9:115626600-115633800	Strong transcription	Liver	Liver
21	chr9:115627000-115647000	Weak transcription	Colonic Mucosa	Colon
22	chr9:115627200-115637200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr9:115627400-115633200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr9:115627600-115642000	Weak transcription	Primary hematopoietic stem cells	blood
25	chr9:115627600-115646800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr9:115627800-115640600	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr9:115628400-115633400	Strong transcription	Brain Inferior Temporal Lobe	brain
28	chr9:115628600-115640800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr9:115629200-115633200	Enhancers	HepG2	liver
30	chr9:115629400-115633400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr9:115630000-115633600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr9:115630200-115633000	Strong transcription	Left Ventricle	heart
33	chr9:115630200-115633200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr9:115630200-115633200	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr9:115630200-115633200	Strong transcription	Fetal Brain Female	brain
36	chr9:115630200-115633200	Strong transcription	Right Ventricle	heart
37	chr9:115630200-115633400	Genic enhancers	Primary B cells from cord blood	blood
38	chr9:115630200-115633400	Strong transcription	Brain Angular Gyrus	brain
39	chr9:115630200-115633400	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr9:115630200-115633600	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr9:115630400-115633000	Strong transcription	Aorta	Aorta
42	chr9:115630400-115633000	Strong transcription	Brain Cingulate Gyrus	brain
43	chr9:115630600-115633800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr9:115630600-115634200	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr9:115630600-115634800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr9:115630600-115636400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr9:115630600-115642000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr9:115630600-115643400	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr9:115630600-115646400	Weak transcription	Fetal Lung	lung
50	chr9:115630600-115647200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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