Variant report

Variant	rs6796222
Chromosome Location	chr3:120448680-120448681
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	chr3:120447002..120449223-chr3:120459526..120461842,3	MCF-7	breast:
2	chr3:120447696..120450299-chr3:120461200..120463686,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144840	Chromatin interaction
ENSG00000153767	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];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11714961	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12489104	0.84[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap]
rs13316584	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1566988	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs167722	0.80[ASN][1000 genomes]
rs172819	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs178725	0.82[ASN][1000 genomes]
rs2288096	0.84[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
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];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs373188	0.82[ASN][1000 genomes]
rs417061	0.83[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs4501055	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs519336	0.83[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs55831173	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56406902	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs607953	0.83[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs618642	0.83[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs6778859	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73183726	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[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];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7633399	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]
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];0.97[EUR][1000 genomes];0.94[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];0.98[EUR][1000 genomes];0.94[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];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9872831	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[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];1.00[EUR][1000 genomes];0.98[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
rs6796222	FSTL1	cis	parietal	SCAN
rs6796222	STXBP5L	cis	cerebellum	SCAN
rs6796222	ALDH1L1	cis	parietal	SCAN
rs6796222	UMPS	cis	cerebellum	SCAN
rs6796222	SLC41A3	cis	cerebellum	SCAN

Chromatin state (count:84 , 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	chr3:120423000-120460200	Weak transcription	HUVEC	blood vessel
7	chr3:120424600-120450200	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr3:120425000-120451200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr3:120425000-120456600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr3:120428600-120449200	Weak transcription	Placenta	Placenta
11	chr3:120429200-120456200	Weak transcription	Liver	Liver
12	chr3:120438400-120449600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr3:120438400-120456200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr3:120438400-120457600	Weak transcription	Fetal Lung	lung
15	chr3:120438400-120460200	Weak transcription	NHEK	skin
16	chr3:120438400-120460600	Weak transcription	Brain Anterior Caudate	brain
17	chr3:120438400-120460600	Weak transcription	Right Ventricle	heart
18	chr3:120438600-120448800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:120438600-120449000	Weak transcription	Adipose Nuclei	Adipose
20	chr3:120438600-120449200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr3:120438600-120449200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:120438600-120449400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr3:120438600-120449400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:120438600-120450200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:120438600-120451600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr3:120438600-120456200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:120438600-120456400	Weak transcription	Left Ventricle	heart
28	chr3:120438600-120456600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:120438600-120457000	Weak transcription	Spleen	Spleen
30	chr3:120438600-120457200	Weak transcription	Pancreas	Pancrea
31	chr3:120438600-120460000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr3:120438600-120460400	Weak transcription	Rectal Smooth Muscle	rectum
33	chr3:120439000-120456400	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr3:120439000-120456600	Weak transcription	Lung	lung
35	chr3:120439000-120457000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr3:120439000-120460200	Weak transcription	Primary B cells from cord blood	blood
37	chr3:120439200-120460200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:120439800-120460200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr3:120441200-120456600	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr3:120441200-120456600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr3:120441400-120449800	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr3:120441400-120450000	Weak transcription	Fetal Muscle Trunk	muscle
43	chr3:120441400-120460000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr3:120441600-120449400	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr3:120441600-120456600	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr3:120441600-120457000	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr3:120442600-120460400	Weak transcription	Brain Substantia Nigra	brain
48	chr3:120443600-120451800	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr3:120443800-120456000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr3:120443800-120460200	Weak transcription	HSMM	muscle

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