Variant report

Variant	rs10260250
Chromosome Location	chr7:106947123-106947124
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1015410	0.87[CEU][hapmap]
rs1024401	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs10249326	0.92[EUR][1000 genomes]
rs10264687	0.86[EUR][1000 genomes]
rs1034734	0.88[EUR][1000 genomes]
rs12333638	0.86[ASN][1000 genomes]
rs12532293	0.87[EUR][1000 genomes]
rs2107762	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2107763	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2158347	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.81[ASN][1000 genomes]
rs2189500	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2214679	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2237663	0.80[EUR][1000 genomes]
rs2237667	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2250410	0.81[CEU][hapmap]
rs2269970	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2395836	0.84[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap]
rs2395839	0.92[CEU][hapmap]
rs2520279	0.88[CEU][hapmap];0.89[TSI][hapmap]
rs257376	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs257384	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap]
rs2712192	0.88[CEU][hapmap]
rs2712194	0.88[CEU][hapmap]
rs28718577	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4727674	0.90[EUR][1000 genomes]
rs4727675	0.87[EUR][1000 genomes]
rs4727682	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4730221	0.92[CEU][hapmap];0.84[TSI][hapmap]
rs4730230	0.83[EUR][1000 genomes]
rs4730244	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs57784799	0.85[EUR][1000 genomes]
rs57815418	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6466163	0.86[EUR][1000 genomes]
rs6466164	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6466165	0.92[EUR][1000 genomes]
rs6954422	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6966616	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6969719	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs6971864	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7357192	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7787113	0.88[CEU][hapmap]
rs7789927	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7791955	0.85[CEU][hapmap]
rs7794142	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7794437	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7794896	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7802375	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7804398	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3383027	chr7:106802625-107096474	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv888939	chr7:106849393-107045700	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1016691	chr7:106880953-106960515	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1015615	chr7:106888529-106962332	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv1024903	chr7:106897237-106965091	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv1034707	chr7:106897237-106966215	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	esv1825788	chr7:106897237-107136320	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv1024793	chr7:106900877-107170312	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv1033064	chr7:106903099-106949640	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	esv1797664	chr7:106930295-106964433	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10260250	COG5	cis	cerebellum	SCAN
rs10260250	PSMC2	cis	cerebellum	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:106886400-106971400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr7:106888800-106999400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr7:106904800-106959800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr7:106909000-106968600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr7:106911000-106964200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr7:106915200-106953400	Weak transcription	Left Ventricle	heart
7	chr7:106918600-106963800	Weak transcription	HSMM	muscle
8	chr7:106923000-106965800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr7:106923800-106999400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr7:106925600-106959800	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr7:106928000-106958800	Weak transcription	HepG2	liver
12	chr7:106928000-106972600	Weak transcription	Fetal Muscle Leg	muscle
13	chr7:106931400-106962800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr7:106932200-106967400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr7:106932400-106955600	Weak transcription	Stomach Mucosa	stomach
16	chr7:106932400-106956200	Weak transcription	HMEC	breast
17	chr7:106932600-106953400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr7:106934200-106947400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr7:106934200-106967400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr7:106934200-106968600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr7:106934200-106971600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr7:106934200-106973000	Weak transcription	Adipose Nuclei	Adipose
23	chr7:106934400-106967200	Weak transcription	Fetal Stomach	stomach
24	chr7:106934400-106971400	Weak transcription	Ovary	ovary
25	chr7:106934800-106962400	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr7:106935200-106962400	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr7:106935400-106964000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr7:106937400-106952800	Weak transcription	NH-A	brain
29	chr7:106938400-106960000	Weak transcription	Primary B cells from peripheral blood	blood
30	chr7:106939000-106962400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr7:106943000-106973000	Weak transcription	Thymus	Thymus
32	chr7:106943200-106950400	Weak transcription	Fetal Heart	heart
33	chr7:106944800-106948000	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr7:106945400-106947600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr7:106945600-106953000	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr7:106945800-106960200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr7:106945800-106973000	Weak transcription	Right Ventricle	heart
38	chr7:106946200-106967200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr7:106946200-106999800	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr7:106946400-106947200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr7:106946400-106947400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr7:106946400-106947400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr7:106946400-106947600	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr7:106946400-106949400	Weak transcription	K562	blood
45	chr7:106946400-106953000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr7:106946400-106953400	Weak transcription	Primary B cells from cord blood	blood
47	chr7:106946400-106960200	Weak transcription	Primary hematopoietic stem cells	blood
48	chr7:106946400-106960800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr7:106946400-106962400	Weak transcription	Liver	Liver
50	chr7:106946400-106962600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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