Variant report

Variant	rs12534816
Chromosome Location	chr7:26385540-26385541
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:26384575..26386800-chr7:26402613..26404629,2	MCF-7	breast:
2	chr7:26330677..26332957-chr7:26384822..26387116,2	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	chr7:26228171..26230631-chr7:26384703..26386781,2	K562	blood:
6	chr7:26385066..26388736-chr7:26388870..26392528,4	K562	blood:
7	chr7:26226466..26228099-chr7:26385363..26387499,2	K562	blood:

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

Extended variants
information (count: 52 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10230728	0.89[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs10231242	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10231349	0.83[ASN][1000 genomes]
rs10235391	0.83[ASN][1000 genomes]
rs10238493	0.87[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs10238702	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10238717	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10246401	0.84[ASN][1000 genomes]
rs10252532	0.86[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs10254065	0.87[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs10260489	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10267867	0.83[ASN][1000 genomes]
rs10270099	0.86[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs10270279	0.84[ASN][1000 genomes]
rs10281957	0.82[CEU][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10951130	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12532077	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12532454	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs12532473	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs12534835	0.89[CEU][hapmap];0.87[TSI][hapmap]
rs12535203	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs12537520	0.80[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12537599	0.87[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs12666571	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12669655	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12670125	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13243295	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13243466	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13244200	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17153471	0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs1852859	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1852860	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2014728	0.91[CEU][hapmap]
rs2014729	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2014735	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2391270	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs2391276	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs35042524	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35749074	0.83[ASN][1000 genomes]
rs3757665	0.81[ASN][1000 genomes]
rs3757666	0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs3801890	0.89[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs3801891	0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs3823943	0.91[JPT][hapmap]
rs4506105	0.86[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs61558019	0.83[ASN][1000 genomes]
rs6947348	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7784736	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12534816	SNX10	cis	lymphoblastoid	seeQTL
rs12534816	CPVL	cis	cerebellum	SCAN
rs12534816	STK31	cis	cerebellum	SCAN
rs12534816	OSBPL3	cis	cerebellum	SCAN
rs12534816	PCP4L1	trans	parietal	SCAN
rs12534816	NFE2L3	cis	parietal	SCAN
rs12534816	LOC441204	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

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	chr7:26368800-26405000	Weak transcription	Placenta	Placenta
4	chr7:26372400-26405200	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr7:26374400-26386200	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr7:26374800-26386200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr7:26375000-26414000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr7:26375200-26386200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr7:26376400-26385800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr7:26377400-26385600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr7:26377600-26386000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr7:26377800-26386200	Weak transcription	GM12878-XiMat	blood
13	chr7:26379000-26386200	Weak transcription	Fetal Intestine Small	intestine
14	chr7:26380400-26386000	Weak transcription	Primary T cells from cord blood	blood
15	chr7:26381000-26386200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr7:26382000-26386600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr7:26382400-26386200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr7:26382400-26386200	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr7:26382600-26387000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr7:26382600-26388000	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr7:26382600-26392000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr7:26382600-26393400	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr7:26382800-26392800	Strong transcription	Primary B cells from cord blood	blood
24	chr7:26383600-26385800	Weak transcription	Dnd41	blood
25	chr7:26384000-26385600	Weak transcription	Lung	lung
26	chr7:26384000-26387600	Enhancers	Liver	Liver
27	chr7:26384000-26389400	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr7:26384400-26385600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr7:26384400-26386200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr7:26384400-26386200	Weak transcription	Adipose Nuclei	Adipose
31	chr7:26384600-26386400	Weak transcription	Brain Angular Gyrus	brain
32	chr7:26384600-26389000	Enhancers	HepG2	liver
33	chr7:26384600-26391200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr7:26384600-26393000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr7:26384800-26385600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr7:26384800-26386600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr7:26384800-26388600	Strong transcription	Fetal Thymus	thymus
38	chr7:26384800-26409400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr7:26385000-26385600	Enhancers	Spleen	Spleen
40	chr7:26385000-26386400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr7:26385000-26386800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr7:26385000-26388200	Weak transcription	Fetal Brain Female	brain
43	chr7:26385000-26388800	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr7:26385000-26389600	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr7:26385200-26386200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr7:26385200-26387000	Weak transcription	Fetal Intestine Large	intestine
47	chr7:26385200-26387600	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr7:26385200-26390200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr7:26385200-26391200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr7:26385200-26393000	Strong transcription	Primary B cells from peripheral blood	blood

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