Variant report

Variant	rs9320287
Chromosome Location	chr6:109744690-109744691
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	chr6:109742336..109749135-chr6:109759459..109767338,11	MCF-7	breast:
2	chr6:109744187..109748407-chr6:109760095..109763715,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185250	Chromatin interaction
ENSG00000135587	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10080429	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1040284	0.92[EUR][1000 genomes]
rs10457190	0.91[EUR][1000 genomes]
rs1048203	0.95[CEU][hapmap];0.93[GIH][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs10499053	0.90[CEU][hapmap];0.88[GIH][hapmap]
rs1074765	0.83[MKK][hapmap]
rs1074766	0.84[MKK][hapmap]
rs10782161	0.95[EUR][1000 genomes]
rs10782162	0.90[CEU][hapmap];0.88[GIH][hapmap];0.82[EUR][1000 genomes]
rs10872032	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10872034	0.82[EUR][1000 genomes]
rs11153171	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs11153174	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs11153175	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs11153176	0.92[EUR][1000 genomes]
rs11153177	0.95[EUR][1000 genomes]
rs11153180	0.95[EUR][1000 genomes]
rs11153181	0.95[EUR][1000 genomes]
rs11753645	0.80[CEU][hapmap]
rs11967108	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs12190920	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs12190996	0.86[EUR][1000 genomes]
rs12192847	0.87[EUR][1000 genomes]
rs12193493	0.92[EUR][1000 genomes]
rs12197114	0.95[CEU][hapmap];0.83[JPT][hapmap];0.95[EUR][1000 genomes]
rs12206928	0.89[EUR][1000 genomes]
rs12208933	0.90[CEU][hapmap]
rs12209691	0.87[EUR][1000 genomes]
rs12213313	0.95[EUR][1000 genomes]
rs12524273	0.93[EUR][1000 genomes]
rs12524639	0.95[CEU][hapmap];0.83[JPT][hapmap];0.93[EUR][1000 genomes]
rs12528712	0.81[CEU][hapmap]
rs12528822	0.95[CEU][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs13195517	0.81[CEU][hapmap]
rs13199519	0.85[CEU][hapmap]
rs13212766	0.91[EUR][1000 genomes]
rs1322816	0.92[EUR][1000 genomes]
rs1358997	0.93[EUR][1000 genomes]
rs1358998	0.95[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs1546980	0.89[EUR][1000 genomes]
rs1590306	0.92[EUR][1000 genomes]
rs17070580	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17070591	0.86[YRI][hapmap]
rs1923725	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs2236582	0.90[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes]
rs2275650	0.95[CEU][hapmap];0.93[GIH][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs34202013	0.91[EUR][1000 genomes]
rs35056702	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36035949	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36099706	0.95[EUR][1000 genomes]
rs3757234	0.95[CEU][hapmap];0.83[JPT][hapmap];0.93[EUR][1000 genomes]
rs3757235	0.83[MKK][hapmap]
rs3778475	0.92[EUR][1000 genomes]
rs3778477	0.88[EUR][1000 genomes]
rs3799835	0.81[CEU][hapmap]
rs3799839	0.93[EUR][1000 genomes]
rs3807005	0.87[EUR][1000 genomes]
rs3818934	0.91[EUR][1000 genomes]
rs59056467	0.83[EUR][1000 genomes]
rs59906308	0.94[EUR][1000 genomes]
rs68042406	0.83[EUR][1000 genomes]
rs6911838	0.90[CEU][hapmap]
rs6914498	0.90[CEU][hapmap]
rs6920962	0.91[CEU][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6929023	0.93[EUR][1000 genomes]
rs730089	0.82[MKK][hapmap]
rs736830	0.84[MKK][hapmap]
rs7372	0.92[EUR][1000 genomes]
rs752262	0.89[EUR][1000 genomes]
rs7773095	0.95[CEU][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs9480933	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9480948	0.95[CEU][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs9480951	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9480953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9480955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9480957	0.95[CEU][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs9487068	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9487094	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9487095	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9487097	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9487098	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9487100	0.95[CEU][hapmap];0.82[JPT][hapmap];0.95[EUR][1000 genomes]
rs9487103	0.84[MKK][hapmap]
rs974034	0.83[MKK][hapmap]
rs9885646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs9320287	SMPD2	cis	cerebellum	SCAN
rs9320287	SMPD2	cis	Whole Blood	GTEx
rs9320287	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL
rs9320287	SMPD2	cis	parietal	SCAN
rs9320287	MICAL1	Cis_1M	lymphoblastoid	RTeQTL
rs9320287	CD164	cis	parietal	SCAN
rs9320287	ZBTB24	cis	cerebellum	SCAN
rs9320287	MICAL1	cis	parietal	SCAN
rs9320287	PDSS2	cis	cerebellum	SCAN
rs9320287	AKD1	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109705000-109745200	Weak transcription	Fetal Kidney	kidney
2	chr6:109707000-109755400	Weak transcription	Fetal Intestine Small	intestine
3	chr6:109721200-109760600	Weak transcription	Fetal Brain Female	brain
4	chr6:109724400-109750400	Weak transcription	Ovary	ovary
5	chr6:109725800-109760800	Weak transcription	Brain Anterior Caudate	brain
6	chr6:109731400-109745200	Weak transcription	Pancreas	Pancrea
7	chr6:109735200-109750200	Weak transcription	Fetal Muscle Leg	muscle
8	chr6:109735600-109750000	Weak transcription	Brain Hippocampus Middle	brain
9	chr6:109736600-109760800	Weak transcription	Brain Angular Gyrus	brain
10	chr6:109737000-109745400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:109737000-109745400	Weak transcription	Left Ventricle	heart
12	chr6:109737400-109750200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr6:109740400-109754800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr6:109741800-109744800	Enhancers	Placenta	Placenta
15	chr6:109742200-109745200	Weak transcription	NHEK	skin
16	chr6:109742400-109745200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:109742400-109745200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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