Variant report

Variant	rs10230728
Chromosome Location	chr7:26386812-26386813
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:26330677..26332957-chr7:26384822..26387116,2	MCF-7	breast:
2	chr7:26386222..26388194-chr7:26390840..26392963,3	MCF-7	breast:
3	chr7:26240262..26243244-chr7:26384656..26387797,3	MCF-7	breast:
4	chr7:26238981..26240863-chr7:26385040..26387955,2	MCF-7	breast:
5	chr7:26385066..26388736-chr7:26388870..26392528,4	K562	blood:
6	chr7:26226466..26228099-chr7:26385363..26387499,2	K562	blood:

Variant related genes	Relation type
ENSG00000122566	Chromatin interaction
ENSG00000086300	Chromatin interaction
ENSG00000122565	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10231242	0.83[ASN][1000 genomes]
rs10231349	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10235391	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10238493	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10238702	0.95[JPT][hapmap]
rs10238717	0.83[ASN][1000 genomes]
rs10246401	0.90[CEU][hapmap];0.81[CHB][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10252532	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10254065	0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10260489	0.83[ASN][1000 genomes]
rs10267867	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10270099	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]
rs10270279	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10281957	0.82[ASN][1000 genomes]
rs10951130	0.89[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs12532077	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs12532454	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12532473	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12534816	0.89[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs12535203	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12537520	0.84[ASN][1000 genomes]
rs12537599	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12666571	0.83[ASN][1000 genomes]
rs12669655	0.83[ASN][1000 genomes]
rs13243295	0.83[ASN][1000 genomes]
rs13243466	0.83[ASN][1000 genomes]
rs13244200	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs17153471	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17153475	0.87[CEU][hapmap];0.80[GIH][hapmap];0.91[TSI][hapmap]
rs1852859	0.80[ASN][1000 genomes]
rs1852860	0.87[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs2014729	0.87[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2014735	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs2391270	0.91[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2391276	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35042524	0.82[ASN][1000 genomes]
rs35749074	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3757664	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3757665	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3757666	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3801888	0.87[CEU][hapmap]
rs3801890	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3801891	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3823943	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]
rs4506105	0.96[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61558019	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6947348	0.84[ASN][1000 genomes]
rs7784736	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10230728	SNX10	cis	lymphoblastoid	seeQTL
rs10230728	LOC441204	cis	cerebellum	SCAN

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

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	chr7:26382600-26387000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr7:26382600-26388000	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr7:26382600-26392000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr7:26382600-26393400	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr7:26382800-26392800	Strong transcription	Primary B cells from cord blood	blood
9	chr7:26384000-26387600	Enhancers	Liver	Liver
10	chr7:26384000-26389400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr7:26384600-26389000	Enhancers	HepG2	liver
12	chr7:26384600-26391200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr7:26384600-26393000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr7:26384800-26388600	Strong transcription	Fetal Thymus	thymus
15	chr7:26384800-26409400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr7:26385000-26388200	Weak transcription	Fetal Brain Female	brain
17	chr7:26385000-26388800	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr7:26385000-26389600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr7:26385200-26387000	Weak transcription	Fetal Intestine Large	intestine
20	chr7:26385200-26387600	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr7:26385200-26390200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr7:26385200-26391200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr7:26385200-26393000	Strong transcription	Primary B cells from peripheral blood	blood
24	chr7:26385600-26387200	Enhancers	Esophagus	oesophagus
25	chr7:26385600-26389000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr7:26385600-26390000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr7:26385600-26414200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr7:26385800-26387200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr7:26385800-26388200	Strong transcription	Dnd41	blood
30	chr7:26385800-26388600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr7:26386000-26387200	Enhancers	HMEC	breast
32	chr7:26386000-26390000	Strong transcription	Primary hematopoietic stem cells	blood
33	chr7:26386000-26390200	Strong transcription	Primary T cells from cord blood	blood
34	chr7:26386200-26387000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr7:26386200-26387200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr7:26386200-26387800	Genic enhancers	GM12878-XiMat	blood
37	chr7:26386200-26388000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr7:26386200-26388200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr7:26386200-26388200	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr7:26386200-26388200	Strong transcription	Spleen	Spleen
41	chr7:26386400-26387000	Enhancers	Muscle Satellite Cultured Cells	--
42	chr7:26386400-26387000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr7:26386400-26387200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr7:26386400-26387800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr7:26386400-26391800	Weak transcription	K562	blood
46	chr7:26386600-26387000	Flanking Active TSS	NHEK	skin
47	chr7:26386600-26387600	Weak transcription	Brain Angular Gyrus	brain
48	chr7:26386600-26387600	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr7:26386600-26387800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr7:26386600-26405200	Weak transcription	Thymus	Thymus

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