Variant report

Variant	rs10868072
Chromosome Location	chr9:86534480-86534481
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:86533963-86534536	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr9:86532204-86536815	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:86236616..86242493-chr9:86533666..86537484,7	MCF-7	breast:
2	chr9:86533247..86537973-chr9:86593370..86597981,20	MCF-7	breast:
3	chr9:86431003..86433746-chr9:86534377..86536332,2	K562	blood:
4	chr9:86533593..86537892-chr9:86593047..86598677,10	K562	blood:
5	chr9:86534003..86537844-chr9:86570557..86574103,8	K562	blood:
6	chr9:86531254..86532896-chr9:86534357..86536311,2	MCF-7	breast:
7	chr9:86321510..86324086-chr9:86534187..86535894,2	K562	blood:
8	chr9:86529939..86532744-chr9:86534062..86535993,2	MCF-7	breast:
9	chr9:86533979..86537502-chr9:86594012..86596999,11	MCF-7	breast:

No data

Variant related genes	Relation type
KIF27	TF binding region
ENSG00000165113	Chromatin interaction
ENSG00000178966	Chromatin interaction
ENSG00000135018	Chromatin interaction
ENSG00000165119	Chromatin interaction
ENSG00000148057	Chromatin interaction
ENSG00000254473	Chromatin interaction
ENSG00000165118	Chromatin interaction
ENSG00000165115	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10868069	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140284	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11140298	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12001293	0.82[CEU][hapmap];0.91[GIH][hapmap];0.92[TSI][hapmap]
rs12001505	0.82[AMR][1000 genomes]
rs12001918	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12003101	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs12003500	0.82[AMR][1000 genomes]
rs12552069	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17064724	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs17086750	0.82[CEU][hapmap];0.91[GIH][hapmap];0.92[TSI][hapmap]
rs2184086	0.94[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34690696	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35784768	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4480186	0.91[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs55654273	0.82[AMR][1000 genomes]
rs55872219	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56055736	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs57267691	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57531526	0.82[AMR][1000 genomes]
rs57957686	0.81[AMR][1000 genomes]
rs58248061	0.82[AMR][1000 genomes]
rs58474042	0.84[EUR][1000 genomes]
rs60277614	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61490202	0.82[AMR][1000 genomes]
rs7021609	0.90[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap]
rs7027121	0.90[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap]
rs7036293	0.81[EUR][1000 genomes]
rs7038235	0.83[EUR][1000 genomes]
rs7040843	0.82[AMR][1000 genomes]
rs7041687	0.84[AMR][1000 genomes]
rs7045525	0.87[CEU][hapmap];0.80[YRI][hapmap]
rs7046229	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7048626	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs73463313	0.82[AMR][1000 genomes]
rs73463327	0.82[AMR][1000 genomes]
rs73463379	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73463395	0.84[EUR][1000 genomes]
rs73469343	0.92[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7850288	0.82[AMR][1000 genomes]
rs7850404	0.82[AMR][1000 genomes]
rs7850640	0.83[EUR][1000 genomes]
rs7853625	0.81[ASW][hapmap];0.87[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.88[YRI][hapmap]
rs7854432	0.83[EUR][1000 genomes]
rs7856614	0.94[CEU][hapmap];0.80[YRI][hapmap]
rs7857619	0.87[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7859830	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7867221	0.94[CEU][hapmap];0.80[YRI][hapmap]
rs7874481	0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9695726	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs970846	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.85[EUR][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	nsv469859	chr9:86398152-86587957	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv482641	chr9:86398152-86587957	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	esv2758192	chr9:86414024-86603602	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2759701	chr9:86414024-86603602	Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv8541	chr9:86469723-86593758	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	nsv438108	chr9:86488586-86542206	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases
7	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10868072	RMI1	cis	parietal	SCAN
rs10868072	C4orf31	trans	lymphoblastoid	RTeQTL

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86461600-86535400	Weak transcription	Fetal Intestine Small	intestine
2	chr9:86461600-86535400	Weak transcription	Ovary	ovary
3	chr9:86462200-86535200	Weak transcription	Fetal Brain Female	brain
4	chr9:86462600-86535200	Weak transcription	Brain Anterior Caudate	brain
5	chr9:86481000-86535800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr9:86491000-86535200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr9:86491200-86535200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr9:86496000-86535000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr9:86499400-86535000	Weak transcription	Fetal Kidney	kidney
10	chr9:86500000-86534800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr9:86500200-86535200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr9:86500200-86535200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr9:86500200-86535600	Weak transcription	Lung	lung
14	chr9:86502600-86535000	Weak transcription	Fetal Lung	lung
15	chr9:86506400-86534800	Weak transcription	Pancreas	Pancrea
16	chr9:86508200-86535600	Weak transcription	Esophagus	oesophagus
17	chr9:86512400-86535400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr9:86512600-86535400	Weak transcription	Placenta	Placenta
19	chr9:86513200-86534800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr9:86516200-86535000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr9:86517400-86535200	Weak transcription	Primary B cells from peripheral blood	blood
22	chr9:86517600-86535000	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr9:86518800-86535000	Weak transcription	Primary B cells from cord blood	blood
24	chr9:86518800-86535000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr9:86518800-86535200	Weak transcription	Thymus	Thymus
26	chr9:86519000-86535000	Weak transcription	Fetal Muscle Leg	muscle
27	chr9:86519000-86535400	Weak transcription	Fetal Stomach	stomach
28	chr9:86520400-86535400	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr9:86523800-86535000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr9:86523800-86535000	Weak transcription	Fetal Muscle Trunk	muscle
31	chr9:86525000-86535000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr9:86525600-86535000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr9:86525600-86535600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr9:86525600-86535600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr9:86526400-86535200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr9:86527200-86535000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr9:86528600-86535000	Weak transcription	Fetal Intestine Large	intestine
38	chr9:86531200-86535000	Weak transcription	NHEK	skin
39	chr9:86531600-86535200	Weak transcription	Osteobl	bone
40	chr9:86531600-86535400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr9:86531800-86535200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr9:86532200-86535200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr9:86532400-86534600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr9:86532400-86535000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr9:86532400-86535000	Weak transcription	Hela-S3	cervix
46	chr9:86532400-86535200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr9:86532400-86535200	Weak transcription	Brain Hippocampus Middle	brain
48	chr9:86532600-86534800	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr9:86532800-86535200	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr9:86532800-86535400	Weak transcription	Psoas Muscle	Psoas

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