Variant report

Variant	rs1323768
Chromosome Location	chr9:85814800-85814801
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:85813794..85816602-chr9:85833659..85835490,2	MCF-7	breast:
2	chr9:85722110..85725029-chr9:85812448..85815231,2	MCF-7	breast:
3	chr9:85814102..85814822-chr9:85845756..85846542,4	MCF-7	breast:
4	chr9:85800689..85803340-chr9:85812087..85815667,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229109	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10114830	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10117817	0.81[ASN][1000 genomes]
rs10122684	0.81[ASN][1000 genomes]
rs10122802	0.81[ASN][1000 genomes]
rs10735561	0.81[ASN][1000 genomes]
rs10746698	0.81[ASN][1000 genomes]
rs10746699	0.81[ASN][1000 genomes]
rs10780577	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10780578	0.83[ASN][1000 genomes]
rs10780579	0.83[ASN][1000 genomes]
rs11139957	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1323767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1535747	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1535748	0.83[ASN][1000 genomes]
rs1830771	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1924239	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2209191	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4390021	0.81[ASN][1000 genomes]
rs4877741	0.81[ASN][1000 genomes]
rs4877742	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4877744	0.81[ASN][1000 genomes]
rs4877746	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4877750	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6559711	0.87[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6559715	0.81[ASN][1000 genomes]
rs7028221	0.81[ASN][1000 genomes]
rs7030390	0.81[ASN][1000 genomes]
rs7043458	0.81[ASN][1000 genomes]
rs744959	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs748415	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7848473	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7851447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7851474	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7855633	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7866798	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7871379	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8181116	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893511	chr9:85495968-85833127	Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv831642	chr9:85679425-85817338	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1323768	RMI1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:85812600-85815000	Enhancers	Fetal Stomach	stomach
2	chr9:85813600-85815800	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr9:85813800-85814800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr9:85813800-85816000	Weak transcription	Brain Germinal Matrix	brain
5	chr9:85814000-85815000	Enhancers	Fetal Brain Female	brain
6	chr9:85814200-85814800	Enhancers	Brain Angular Gyrus	brain
7	chr9:85814200-85815200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr9:85814400-85814800	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr9:85814800-85815600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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