Variant report

Variant	rs9480956
Chromosome Location	chr6:109745508-109745509
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:109742336..109749135-chr6:109759459..109767338,11	MCF-7	breast:
2	chr6:109744187..109748407-chr6:109760095..109763715,4	MCF-7	breast:
3	chr6:109744870..109747846-chr6:109748398..109750532,2	K562	blood:

Variant related genes	Relation type
ENSG00000135587	Chromatin interaction
ENSG00000185250	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10457192	0.88[CEU][hapmap]
rs10457194	0.88[CEU][hapmap]
rs10457195	0.88[CEU][hapmap]
rs1046943	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1054607	0.94[YRI][hapmap]
rs1074765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1074766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10872033	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11153183	0.88[CEU][hapmap]
rs11251	0.96[CEU][hapmap];0.82[JPT][hapmap];0.91[EUR][1000 genomes]
rs11754455	0.88[CEU][hapmap]
rs11755641	0.88[CEU][hapmap]
rs12194061	0.88[CEU][hapmap]
rs12197180	0.88[CEU][hapmap]
rs12198938	0.88[CEU][hapmap]
rs12199154	0.88[CEU][hapmap]
rs12212476	0.88[CEU][hapmap]
rs12214147	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12529733	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13219952	0.92[EUR][1000 genomes]
rs13220915	0.88[CEU][hapmap]
rs1406899	0.88[CEU][hapmap]
rs1476387	1.00[CEU][hapmap];0.82[JPT][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1521907	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17070591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1853330	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1885690	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1885691	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1980591	0.87[CEU][hapmap]
rs2024850	0.88[CEU][hapmap]
rs2024853	0.88[CEU][hapmap]
rs2211288	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2236084	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes]
rs2277113	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2277114	0.88[CEU][hapmap]
rs2884037	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35146243	0.91[EUR][1000 genomes]
rs3734652	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3757230	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3757231	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3757235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3778474	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs3778478	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3799842	0.96[CEU][hapmap];0.81[YRI][hapmap];0.83[EUR][1000 genomes]
rs3818933	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4636056	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4945831	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4946967	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs4946970	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4946976	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58644322	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59597139	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914216	0.91[EUR][1000 genomes]
rs6920372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6920712	0.94[YRI][hapmap]
rs6920962	0.96[CHB][hapmap];0.80[YRI][hapmap]
rs6925005	0.88[YRI][hapmap]
rs6939548	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6939953	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs699700	0.91[EUR][1000 genomes]
rs730089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs736830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs746794	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7748669	0.96[CEU][hapmap];0.82[JPT][hapmap];0.95[EUR][1000 genomes]
rs7751582	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7754650	0.96[CEU][hapmap];0.82[JPT][hapmap];0.93[EUR][1000 genomes]
rs7755941	0.87[CEU][hapmap]
rs7768973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7773950	0.88[CEU][hapmap]
rs8465	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs910730	0.96[CEU][hapmap];0.82[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9320286	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9372213	0.81[CEU][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9398202	0.80[EUR][1000 genomes]
rs9480947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9480949	0.92[EUR][1000 genomes]
rs9480958	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9487064	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9487066	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9487069	0.91[EUR][1000 genomes]
rs9487070	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9487076	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9487084	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9487085	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9487103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs974034	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9791241	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9480956	C6orf199	Cis_1M	lymphoblastoid	RTeQTL
rs9480956	RP11-425D10.10	cis	Whole Blood	GTEx
rs9480956	RP11-425D10.10	cis	Skin Sun Exposed Lower leg	GTEx
rs9480956	SMPD2	cis	Esophagus Mucosa	GTEx
rs9480956	ZBTB24	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109707000-109755400	Weak transcription	Fetal Intestine Small	intestine
2	chr6:109721200-109760600	Weak transcription	Fetal Brain Female	brain
3	chr6:109724400-109750400	Weak transcription	Ovary	ovary
4	chr6:109725800-109760800	Weak transcription	Brain Anterior Caudate	brain
5	chr6:109735200-109750200	Weak transcription	Fetal Muscle Leg	muscle
6	chr6:109735600-109750000	Weak transcription	Brain Hippocampus Middle	brain
7	chr6:109736600-109760800	Weak transcription	Brain Angular Gyrus	brain
8	chr6:109737400-109750200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr6:109740400-109754800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr6:109745200-109745600	Genic enhancers	Pancreas	Pancrea
11	chr6:109745200-109745800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr6:109745200-109745800	Enhancers	Fetal Kidney	kidney
13	chr6:109745200-109745800	Enhancers	HepG2	liver
14	chr6:109745200-109746000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr6:109745200-109746000	Enhancers	Adipose Nuclei	Adipose
16	chr6:109745200-109746200	Enhancers	Stomach Mucosa	stomach
17	chr6:109745200-109746400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:109745200-109746400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:109745200-109746400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr6:109745200-109746600	Enhancers	NHEK	skin
21	chr6:109745200-109747000	Enhancers	Placenta	Placenta
22	chr6:109745400-109745600	Enhancers	Gastric	stomach
23	chr6:109745400-109745800	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr6:109745400-109745800	Enhancers	Esophagus	oesophagus
25	chr6:109745400-109745800	Enhancers	Left Ventricle	heart
26	chr6:109745400-109745800	Enhancers	Spleen	Spleen
27	chr6:109745400-109745800	Enhancers	HMEC	breast
28	chr6:109745400-109746000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr6:109745400-109746200	Enhancers	Osteobl	bone
30	chr6:109745400-109746400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr6:109745400-109746400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr6:109745400-109746400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr6:109745400-109746400	Enhancers	K562	blood
34	chr6:109745400-109746600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr6:109745400-109746800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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