Variant report

Variant	rs3801887
Chromosome Location	chr7:26388888-26388889
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr7:26388736-26388936	MCF10A-Er-Src	breast:	n/a	n/a
2	ESRRA	chr7:26387358-26389003	GM12878	blood:	n/a	n/a

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	chr7:26382800..26384799-chr7:26387254..26389366,2	K562	blood:

Variant related genes	Relation type
SNX10	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12537548	0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12672467	1.00[YRI][hapmap]
rs12674232	1.00[YRI][hapmap]
rs3801883	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73068414	0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs73068436	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs73068463	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73068467	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[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
rs3801887	LOC441204	cis	cerebellum	SCAN
rs3801887	GPNMB	cis	parietal	SCAN

Chromatin state (count:55 , 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	chr7:26382600-26392000	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	chr7:26384000-26389400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr7:26384600-26389000	Enhancers	HepG2	liver
9	chr7:26384600-26391200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr7:26384600-26393000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr7:26384800-26409400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr7:26385000-26389600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr7:26385200-26390200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr7:26385200-26391200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr7:26385200-26393000	Strong transcription	Primary B cells from peripheral blood	blood
16	chr7:26385600-26389000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr7:26385600-26390000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr7:26385600-26414200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr7:26386000-26390000	Strong transcription	Primary hematopoietic stem cells	blood
20	chr7:26386000-26390200	Strong transcription	Primary T cells from cord blood	blood
21	chr7:26386400-26391800	Weak transcription	K562	blood
22	chr7:26386600-26405200	Weak transcription	Thymus	Thymus
23	chr7:26386800-26393200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr7:26386800-26395600	Weak transcription	Fetal Lung	lung
25	chr7:26387000-26390200	Enhancers	Fetal Intestine Large	intestine
26	chr7:26387400-26389800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr7:26387400-26391400	Enhancers	Fetal Intestine Small	intestine
28	chr7:26387400-26409400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr7:26387600-26389000	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr7:26387600-26389800	Enhancers	Fetal Kidney	kidney
31	chr7:26387800-26409400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr7:26388000-26389200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr7:26388000-26389600	Enhancers	Adipose Nuclei	Adipose
34	chr7:26388000-26409400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr7:26388200-26389200	Enhancers	NHEK	skin
36	chr7:26388200-26389400	Weak transcription	Brain Angular Gyrus	brain
37	chr7:26388200-26389800	Enhancers	Fetal Brain Female	brain
38	chr7:26388200-26391200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr7:26388200-26404600	Weak transcription	Dnd41	blood
40	chr7:26388200-26405000	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr7:26388400-26389000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr7:26388400-26389200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr7:26388400-26389400	Weak transcription	Pancreas	Pancrea
44	chr7:26388400-26392200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr7:26388400-26397400	Weak transcription	Spleen	Spleen
46	chr7:26388600-26389000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr7:26388600-26389200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr7:26388600-26389600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr7:26388600-26390600	Strong transcription	GM12878-XiMat	blood
50	chr7:26388600-26395400	Strong transcription	Primary monocytes fromperipheralblood	blood

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