Variant report

Variant	rs3823943
Chromosome Location	chr7:26390496-26390497
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:26385066..26388736-chr7:26388870..26392528,4	K562	blood:
2	chr7:26388712..26391203-chr7:26393919..26396186,2	MCF-7	breast:
3	chr7:26389446..26391389-chr7:26400125..26402977,3	K562	blood:
4	chr7:26389556..26392091-chr7:26400125..26403853,4	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10230728	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10231349	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10235391	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10238493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10238702	0.95[JPT][hapmap]
rs10246401	0.90[CEU][hapmap];0.82[CHB][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10252532	0.87[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10254065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10267867	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10270099	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]
rs10270279	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10951130	0.91[JPT][hapmap]
rs12532077	0.91[JPT][hapmap]
rs12532454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12532473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12534816	0.91[JPT][hapmap]
rs12535203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12537599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13244200	0.91[JPT][hapmap]
rs17153471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17153475	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs1852860	0.91[JPT][hapmap]
rs2014729	0.95[JPT][hapmap]
rs2014735	0.91[JPT][hapmap]
rs2391270	0.87[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2391276	0.92[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35749074	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3757664	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3757665	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3757666	1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3801888	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs3801890	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3801891	0.95[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4506105	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61558019	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
3	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3823943	SNX10	cis	multi-tissue	Pritchard
rs3823943	SNX10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26368800-26405000	Weak transcription	Placenta	Placenta
2	chr7:26372400-26405200	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr7:26375000-26414000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr7:26382600-26392000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr7:26382600-26393400	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr7:26382800-26392800	Strong transcription	Primary B cells from cord blood	blood
7	chr7:26384600-26391200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr7:26384600-26393000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr7:26384800-26409400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr7:26385200-26391200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr7:26385200-26393000	Strong transcription	Primary B cells from peripheral blood	blood
12	chr7:26385600-26414200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr7:26386400-26391800	Weak transcription	K562	blood
14	chr7:26386600-26405200	Weak transcription	Thymus	Thymus
15	chr7:26386800-26393200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr7:26386800-26395600	Weak transcription	Fetal Lung	lung
17	chr7:26387400-26391400	Enhancers	Fetal Intestine Small	intestine
18	chr7:26387400-26409400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr7:26387800-26409400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr7:26388000-26409400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr7:26388200-26391200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr7:26388200-26404600	Weak transcription	Dnd41	blood
23	chr7:26388200-26405000	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr7:26388400-26392200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr7:26388400-26397400	Weak transcription	Spleen	Spleen
26	chr7:26388600-26390600	Strong transcription	GM12878-XiMat	blood
27	chr7:26388600-26395400	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr7:26388600-26396600	Weak transcription	Fetal Thymus	thymus
29	chr7:26388600-26397800	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr7:26388800-26402600	Weak transcription	Liver	Liver
31	chr7:26388800-26405200	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr7:26389000-26393000	Weak transcription	HepG2	liver
33	chr7:26389000-26413200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr7:26389200-26393800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr7:26389200-26395400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr7:26389600-26390600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr7:26389800-26402600	Weak transcription	Pancreas	Pancrea
38	chr7:26390000-26398800	Weak transcription	Primary hematopoietic stem cells	blood
39	chr7:26390000-26399000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr7:26390200-26395800	Weak transcription	Fetal Intestine Large	intestine
41	chr7:26390200-26405000	Weak transcription	Primary T cells from cord blood	blood

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