Variant report

Variant	rs6792827
Chromosome Location	chr3:158545195-158545196
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:158544882..158547801-chr3:158551051..158553794,3	MCF-7	breast:
2	chr3:158527065..158529292-chr3:158543447..158545685,2	K562	blood:

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1548093	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2061617	0.88[CHD][hapmap];0.85[ASN][1000 genomes]
rs41272625	1.00[EUR][1000 genomes]
rs61796809	0.93[AFR][1000 genomes]
rs6793618	0.94[ASW][hapmap];0.82[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73019641	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats 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	31 gene(s)	inside rSNPs	diseases
4	nsv1014255	chr3:158358860-158768542	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv532665	chr3:158370013-158754245	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv948755	chr3:158388780-158672287	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv877692	chr3:158430706-158828643	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv1001450	chr3:158440011-158768399	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv536777	chr3:158440011-158768399	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv877693	chr3:158470321-158583004	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv1006146	chr3:158475824-158625778	Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv592123	chr3:158477796-158625128	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv1002514	chr3:158484027-158673414	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
14	nsv536778	chr3:158484027-158673414	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
15	nsv1014511	chr3:158516495-158715240	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6792827	RARRES1	cis	cerebellum	SCAN
rs6792827	MFSD1	cis	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158520400-158552400	Weak transcription	Stomach Mucosa	stomach
2	chr3:158520800-158545400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:158522400-158550000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:158527800-158554000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:158528000-158547000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:158528000-158549400	Weak transcription	Dnd41	blood
7	chr3:158528600-158549600	Weak transcription	Fetal Kidney	kidney
8	chr3:158528800-158547200	Weak transcription	Psoas Muscle	Psoas
9	chr3:158532200-158551800	Weak transcription	NHEK	skin
10	chr3:158532400-158557800	Weak transcription	Gastric	stomach
11	chr3:158533000-158548000	Weak transcription	Pancreas	Pancrea
12	chr3:158533000-158551000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:158533000-158556400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr3:158533000-158559600	Weak transcription	Right Ventricle	heart
15	chr3:158533200-158547600	Weak transcription	A549	lung
16	chr3:158534400-158550800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:158535400-158550600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr3:158535400-158551200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:158535400-158551200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:158535600-158545600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr3:158535600-158545600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr3:158535600-158545600	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr3:158535600-158546200	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr3:158535600-158546200	Strong transcription	Muscle Satellite Cultured Cells	--
25	chr3:158535600-158546400	Strong transcription	Osteobl	bone
26	chr3:158535600-158548200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:158535600-158548600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:158535600-158550200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:158535600-158550200	Strong transcription	Primary B cells from peripheral blood	blood
30	chr3:158535600-158550600	Strong transcription	Liver	Liver
31	chr3:158535600-158550800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:158535800-158545800	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr3:158535800-158548800	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr3:158535800-158550800	Strong transcription	Primary hematopoietic stem cells	blood
35	chr3:158536400-158545200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr3:158536400-158545600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr3:158536400-158548600	Strong transcription	Placenta	Placenta
38	chr3:158537400-158548600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr3:158537800-158550800	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr3:158537800-158551000	Strong transcription	Adipose Nuclei	Adipose
41	chr3:158537800-158551000	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr3:158538600-158546400	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr3:158539400-158545400	Strong transcription	HSMM	muscle
44	chr3:158540000-158550000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr3:158540800-158545600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:158541000-158548800	Strong transcription	Fetal Intestine Large	intestine
47	chr3:158541600-158552000	Weak transcription	Colonic Mucosa	Colon
48	chr3:158541800-158545200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr3:158541800-158548000	Weak transcription	Aorta	Aorta
50	chr3:158541800-158551200	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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