Variant report

Variant	rs12001293
Chromosome Location	chr9:86612565-86612566
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:86605130..86608071-chr9:86609425..86612751,3	K562	blood:
2	chr9:86612231..86616038-chr9:86617136..86619825,3	K562	blood:
3	chr9:86611159..86613982-chr9:86615279..86618286,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000202523	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10868072	0.82[CEU][hapmap];0.91[GIH][hapmap];0.92[TSI][hapmap]
rs11140298	0.87[GIH][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap]
rs12001918	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs12003101	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs12004444	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12552069	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs17064724	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs17086750	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2184086	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs34690696	0.81[EUR][1000 genomes]
rs35784768	0.81[EUR][1000 genomes]
rs4480186	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs55872219	0.83[EUR][1000 genomes]
rs56055736	0.80[EUR][1000 genomes]
rs58474042	0.85[EUR][1000 genomes]
rs7021609	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs7027121	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs7038235	0.81[EUR][1000 genomes]
rs7045525	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs7046229	0.84[EUR][1000 genomes]
rs7047702	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7048626	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs72749137	0.92[ASN][1000 genomes]
rs73463379	0.82[EUR][1000 genomes]
rs73463395	0.85[EUR][1000 genomes]
rs73469343	0.87[EUR][1000 genomes]
rs7850640	0.84[EUR][1000 genomes]
rs7853625	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs7854432	0.84[EUR][1000 genomes]
rs7856614	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7857619	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs7859830	0.82[EUR][1000 genomes]
rs7867221	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7874481	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs970846	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831644	chr9:86534310-86704395	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv893514	chr9:86584160-86678917	Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	esv3386299	chr9:86608775-86613713	Weak transcription Strong transcription Enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12001293	RMI1	cis	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86596400-86632400	Weak transcription	Spleen	Spleen
2	chr9:86596600-86613400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr9:86596600-86613800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:86596600-86616000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:86596600-86617000	Weak transcription	Lung	lung
6	chr9:86596600-86618200	Weak transcription	Ovary	ovary
7	chr9:86596600-86619600	Weak transcription	Gastric	stomach
8	chr9:86596800-86613200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr9:86596800-86614400	Weak transcription	HSMMtube	muscle
10	chr9:86596800-86616000	Weak transcription	Brain Hippocampus Middle	brain
11	chr9:86596800-86616200	Weak transcription	Brain Angular Gyrus	brain
12	chr9:86596800-86616200	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr9:86596800-86619600	Weak transcription	Small Intestine	intestine
14	chr9:86596800-86621400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr9:86596800-86621600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr9:86597000-86614200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr9:86597000-86616000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr9:86597000-86616000	Weak transcription	Fetal Lung	lung
19	chr9:86597000-86617200	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr9:86597000-86621200	Weak transcription	Stomach Smooth Muscle	stomach
21	chr9:86597000-86621600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr9:86597200-86614200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr9:86597200-86615400	Weak transcription	NHDF-Ad	bronchial
24	chr9:86597200-86616000	Weak transcription	Fetal Kidney	kidney
25	chr9:86597200-86616800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr9:86597200-86619000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr9:86597400-86628800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr9:86597600-86615800	Weak transcription	Fetal Muscle Trunk	muscle
29	chr9:86598000-86615800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr9:86598400-86614200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr9:86598600-86615400	Weak transcription	HUVEC	blood vessel
32	chr9:86598800-86622400	Weak transcription	Brain Germinal Matrix	brain
33	chr9:86602000-86614400	Weak transcription	Primary B cells from peripheral blood	blood
34	chr9:86602000-86616000	Weak transcription	Primary hematopoietic stem cells	blood
35	chr9:86602000-86616000	Weak transcription	Duodenum Mucosa	Duodenum
36	chr9:86602000-86620800	Weak transcription	NHLF	lung
37	chr9:86602000-86623200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr9:86602200-86616000	Weak transcription	HSMM	muscle
39	chr9:86602200-86617400	Weak transcription	Osteobl	bone
40	chr9:86602200-86618000	Weak transcription	NHEK	skin
41	chr9:86602200-86618200	Weak transcription	Placenta	Placenta
42	chr9:86602400-86616000	Weak transcription	Primary B cells from cord blood	blood
43	chr9:86602400-86616000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr9:86602400-86616200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr9:86602400-86618000	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr9:86602400-86627200	Weak transcription	Left Ventricle	heart
47	chr9:86602600-86620000	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr9:86602800-86617400	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr9:86603600-86619600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr9:86603800-86621200	Weak transcription	Hela-S3	cervix

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