Variant report

Variant	rs10270099
Chromosome Location	chr7:26377088-26377089
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	chr7:26375094..26376675-chr7:26376861..26378996,2	K562	blood:

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10230728	0.95[CEU][hapmap];0.81[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10231242	0.87[ASN][1000 genomes]
rs10231349	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10235391	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10238493	0.91[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10238702	0.90[JPT][hapmap]
rs10238717	0.87[ASN][1000 genomes]
rs10246401	0.81[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10252532	0.81[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10254065	0.91[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10260489	0.87[ASN][1000 genomes]
rs10267867	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10270279	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10281957	0.86[ASN][1000 genomes]
rs10951130	0.86[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs12532077	0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs12532454	0.91[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12532473	0.91[CEU][hapmap];0.80[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12534816	0.86[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs12535203	0.91[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12537520	0.84[ASN][1000 genomes]
rs12537599	0.91[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12666571	0.87[ASN][1000 genomes]
rs12669655	0.86[ASN][1000 genomes]
rs12670125	0.83[ASN][1000 genomes]
rs13243295	0.87[ASN][1000 genomes]
rs13243466	0.87[ASN][1000 genomes]
rs13244200	0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs17153471	0.91[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17153475	0.82[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs1852859	0.84[ASN][1000 genomes]
rs1852860	0.89[CHD][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2014729	0.89[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs2014735	0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2391270	0.95[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2391276	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35042524	0.85[ASN][1000 genomes]
rs35749074	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3757664	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3757665	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3757666	0.87[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3801888	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs3801890	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3801891	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3823943	0.91[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4506105	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61558019	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6947348	0.84[ASN][1000 genomes]
rs7784736	0.86[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	nsv1021308	chr7:26116605-26419720	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv1018971	chr7:26161228-26380361	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	nsv1029596	chr7:26302739-26737913	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv538804	chr7:26302739-26737913	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	esv2761313	chr7:26340970-26389772	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10270099	SNX10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26335200-26386400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr7:26345600-26386200	Weak transcription	Thymus	Thymus
3	chr7:26361800-26385400	Weak transcription	Pancreas	Pancrea
4	chr7:26367600-26378800	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr7:26368600-26377600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr7:26368800-26405000	Weak transcription	Placenta	Placenta
7	chr7:26369400-26379600	Weak transcription	HepG2	liver
8	chr7:26370400-26385000	Weak transcription	Spleen	Spleen
9	chr7:26370600-26377400	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr7:26372400-26405200	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr7:26374400-26386200	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr7:26374600-26381000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr7:26374800-26377400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr7:26374800-26382600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr7:26374800-26386200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr7:26375000-26414000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr7:26375200-26380200	Weak transcription	Primary T cells from cord blood	blood
18	chr7:26375200-26385000	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr7:26375200-26386200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr7:26375400-26377800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr7:26375600-26377400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr7:26375800-26377600	Flanking Active TSS	Primary B cells from cord blood	blood
23	chr7:26376000-26377600	Flanking Active TSS	GM12878-XiMat	blood
24	chr7:26376200-26380000	Enhancers	Primary B cells from peripheral blood	blood
25	chr7:26376200-26380000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr7:26376400-26385800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr7:26376600-26379600	Weak transcription	Fetal Kidney	kidney
28	chr7:26376600-26385200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr7:26377000-26377600	Enhancers	Primary hematopoietic stem cells	blood
30	chr7:26377000-26377600	Enhancers	Fetal Lung	lung
31	chr7:26377000-26377800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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