Variant report

Variant	rs7633399
Chromosome Location	chr3:120445849-120445850
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	chr11:62607627..62609431-chr3:120445103..120446974,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133316	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10511404	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11714961	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12489104	0.84[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap]
rs13316584	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1566988	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs167722	0.82[ASN][1000 genomes]
rs172819	0.83[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs178725	0.83[ASN][1000 genomes]
rs2288096	0.84[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs2292719	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs373188	0.83[ASN][1000 genomes]
rs417061	0.83[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs4501055	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs519336	0.83[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs55831173	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56406902	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs607953	0.83[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs618642	0.83[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs6778859	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6796222	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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73183726	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7430785	1.00[YRI][hapmap]
rs7620570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9814744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9838458	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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9854081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9872831	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9985346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv829699	chr3:120308332-120484695	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
4	nsv869548	chr3:120320731-121076337	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv916869	chr3:120360281-120973169	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv877378	chr3:120381530-120606438	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
7	nsv965203	chr3:120441087-120449682	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7633399	SLC41A3	cis	cerebellum	SCAN
rs7633399	STXBP5L	cis	cerebellum	SCAN
rs7633399	FSTL1	cis	parietal	SCAN
rs7633399	ALDH1L1	cis	parietal	SCAN
rs7633399	UMPS	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120402800-120456600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:120416400-120460600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr3:120416800-120460600	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr3:120417600-120456600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr3:120419000-120450800	Weak transcription	Brain Hippocampus Middle	brain
6	chr3:120422200-120446800	Weak transcription	Ovary	ovary
7	chr3:120423000-120460200	Weak transcription	HUVEC	blood vessel
8	chr3:120423600-120447200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:120424400-120446800	Weak transcription	Fetal Intestine Large	intestine
10	chr3:120424600-120450200	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr3:120425000-120451200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr3:120425000-120456600	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr3:120425600-120446600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:120428400-120446800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:120428400-120448000	Weak transcription	Osteobl	bone
16	chr3:120428600-120449200	Weak transcription	Placenta	Placenta
17	chr3:120429200-120456200	Weak transcription	Liver	Liver
18	chr3:120430000-120446600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:120438200-120447600	Weak transcription	GM12878-XiMat	blood
20	chr3:120438400-120446800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr3:120438400-120447000	Weak transcription	Psoas Muscle	Psoas
22	chr3:120438400-120449600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:120438400-120456200	Weak transcription	Stomach Smooth Muscle	stomach
24	chr3:120438400-120457600	Weak transcription	Fetal Lung	lung
25	chr3:120438400-120460200	Weak transcription	NHEK	skin
26	chr3:120438400-120460600	Weak transcription	Brain Anterior Caudate	brain
27	chr3:120438400-120460600	Weak transcription	Right Ventricle	heart
28	chr3:120438600-120446800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr3:120438600-120446800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr3:120438600-120448800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr3:120438600-120449000	Weak transcription	Adipose Nuclei	Adipose
32	chr3:120438600-120449200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr3:120438600-120449200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr3:120438600-120449400	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr3:120438600-120449400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:120438600-120450200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:120438600-120451600	Weak transcription	Duodenum Mucosa	Duodenum
38	chr3:120438600-120456200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:120438600-120456400	Weak transcription	Left Ventricle	heart
40	chr3:120438600-120456600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr3:120438600-120457000	Weak transcription	Spleen	Spleen
42	chr3:120438600-120457200	Weak transcription	Pancreas	Pancrea
43	chr3:120438600-120460000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr3:120438600-120460400	Weak transcription	Rectal Smooth Muscle	rectum
45	chr3:120439000-120456400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr3:120439000-120456600	Weak transcription	Lung	lung
47	chr3:120439000-120457000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr3:120439000-120460200	Weak transcription	Primary B cells from cord blood	blood
49	chr3:120439200-120460200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr3:120439800-120460200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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