Variant report

Variant	rs4548256
Chromosome Location	chr9:115969423-115969424
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	chr9:115968725..115971196-chr9:115981878..115984279,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119321	Chromatin interaction
ENSG00000136868	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10081701	0.86[MKK][hapmap]
rs10114293	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117100	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10118727	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10118914	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10123301	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10817454	0.91[LWK][hapmap]
rs10981662	0.83[AFR][1000 genomes]
rs10981663	0.81[YRI][hapmap]
rs10981672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981682	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10981687	0.88[AFR][1000 genomes]
rs1128786	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs1133618	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1133619	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1133620	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12236187	0.92[ASW][hapmap]
rs12339424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12344443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16910202	1.00[ASW][hapmap];0.95[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs16912536	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16927031	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28790397	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28790632	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28830537	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28887481	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28891677	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3810910	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs4333682	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4378033	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4407968	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4490910	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs5015972	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55660432	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029139	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029228	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029472	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7030027	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7033282	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7034425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7035169	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7038133	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72758243	0.88[AFR][1000 genomes]
rs73550301	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73552213	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73655814	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73655844	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73655845	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7849150	0.95[YRI][hapmap]
rs7850672	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs7852613	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7854882	1.00[YRI][hapmap]
rs7855105	1.00[YRI][hapmap]
rs7860472	0.88[AFR][1000 genomes]
rs7865445	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7865584	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7865650	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7866432	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7874583	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9695716	1.00[YRI][hapmap]
rs9722731	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758198	chr9:115240454-116002951	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759710	chr9:115240454-116002951	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv1035406	chr9:115883978-116003980	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv540201	chr9:115883978-116003980	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised 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	40 gene(s)	inside rSNPs	diseases
8	nsv893745	chr9:115955271-116005783	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv1041112	chr9:115960704-116005783	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4548256	RGS3	cis	parietal	SCAN
rs4548256	SNORD115-38	trans	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115920000-115970200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr9:115920000-115973400	Strong transcription	Rectal Mucosa Donor 29	rectum
3	chr9:115920400-115973400	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr9:115920800-115975000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr9:115923400-115976400	Strong transcription	Primary T cells fromperipheralblood	blood
6	chr9:115924200-115969600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr9:115927600-115973400	Strong transcription	Skeletal Muscle Female	skeletal muscle
8	chr9:115936800-115982400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr9:115945400-115977200	Weak transcription	Stomach Mucosa	stomach
10	chr9:115945600-115982800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr9:115950400-115972800	Weak transcription	Right Ventricle	heart
12	chr9:115950600-115982400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr9:115950800-115982800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr9:115951000-115972200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr9:115951000-115972200	Weak transcription	Gastric	stomach
16	chr9:115951000-115972200	Weak transcription	Pancreas	Pancrea
17	chr9:115951000-115974000	Strong transcription	Placenta	Placenta
18	chr9:115951000-115982800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr9:115952200-115974400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr9:115952400-115973400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr9:115952400-115973600	Strong transcription	Adipose Nuclei	Adipose
22	chr9:115952400-115974400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr9:115954600-115973600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr9:115956000-115973400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr9:115956200-115971800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr9:115956600-115972200	Weak transcription	Aorta	Aorta
27	chr9:115956600-115972200	Weak transcription	Esophagus	oesophagus
28	chr9:115957400-115970000	Strong transcription	HUVEC	blood vessel
29	chr9:115957600-115972000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr9:115957600-115974000	Strong transcription	Duodenum Mucosa	Duodenum
31	chr9:115957800-115970800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr9:115957800-115974400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr9:115957800-115974400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr9:115958000-115974000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr9:115958400-115972400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr9:115958800-115971400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr9:115959000-115969600	Strong transcription	Brain Hippocampus Middle	brain
38	chr9:115959000-115973400	Strong transcription	Fetal Lung	lung
39	chr9:115959800-115970400	Strong transcription	NH-A	brain
40	chr9:115960000-115970400	Weak transcription	Lung	lung
41	chr9:115960600-115973000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr9:115962800-115976800	Weak transcription	Small Intestine	intestine
43	chr9:115963400-115972600	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr9:115963400-115973400	Strong transcription	Liver	Liver
45	chr9:115964000-115976000	Strong transcription	Fetal Brain Female	brain
46	chr9:115964000-115977000	Weak transcription	Psoas Muscle	Psoas
47	chr9:115964200-115971000	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr9:115964800-115970200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr9:115964800-115971800	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr9:115964800-115979200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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