Variant report

Variant	rs9867586
Chromosome Location	chr3:98543301-98543302
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:98543071..98543590-chr3:98712733..98713238,2	MCF-7	breast:
2	chr3:98542228..98544778-chr3:98545790..98547859,2	K562	blood:
3	chr3:98543087..98543918-chr3:98712722..98713277,2	MCF-7	breast:

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1062196	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12107050	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12330170	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12490832	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13060012	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs14310	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1440150	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17270593	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1866677	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1866678	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1866679	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1875086	0.84[EUR][1000 genomes]
rs2028393	0.86[EUR][1000 genomes]
rs2119187	0.80[ASN][1000 genomes]
rs2119188	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2262597	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2290067	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2439213	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2439214	0.82[ASN][1000 genomes]
rs2439215	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2439217	0.83[ASN][1000 genomes]
rs2439218	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2439220	0.80[ASN][1000 genomes]
rs2439222	0.84[EUR][1000 genomes]
rs2439223	0.84[EUR][1000 genomes]
rs2439225	0.85[EUR][1000 genomes]
rs2439228	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2439229	0.88[ASN][1000 genomes]
rs2439231	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2439236	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2454676	0.83[ASN][1000 genomes]
rs2454677	0.84[ASN][1000 genomes]
rs2454678	0.83[ASN][1000 genomes]
rs2454680	0.80[ASN][1000 genomes]
rs2454682	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2454684	0.80[ASN][1000 genomes]
rs2454685	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2470857	0.80[ASN][1000 genomes]
rs2470859	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2470860	0.80[ASN][1000 genomes]
rs2470861	0.80[ASN][1000 genomes]
rs2470864	0.83[ASN][1000 genomes]
rs2470865	0.82[ASN][1000 genomes]
rs2470867	0.88[ASN][1000 genomes]
rs2470869	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2470879	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2470881	0.86[EUR][1000 genomes]
rs28802000	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2919236	0.88[ASN][1000 genomes]
rs2960190	0.81[EUR][1000 genomes]
rs34234373	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs34558202	0.95[ASN][1000 genomes]
rs3755574	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3755576	0.83[ASN][1000 genomes]
rs3772101	0.86[ASN][1000 genomes]
rs3772102	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4425200	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4425201	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4426625	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4426626	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4494869	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs62278486	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6782630	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6785935	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6788418	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6788689	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6804850	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6808116	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs704585	0.86[ASN][1000 genomes]
rs7611929	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7612036	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7616275	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7630800	0.80[ASN][1000 genomes]
rs828609	0.88[ASN][1000 genomes]
rs9811305	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9811449	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9811860	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9814819	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9815226	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9823430	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9845558	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9855175	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9860216	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9860264	0.83[EUR][1000 genomes]
rs9873932	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9878392	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9881519	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9883516	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9883537	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs999147	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv1009032	chr3:98514221-98607721	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9867586	ST3GAL6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98503400-98576400	Weak transcription	Gastric	stomach
2	chr3:98516800-98544000	Weak transcription	Spleen	Spleen
3	chr3:98523800-98543800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:98524000-98543600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:98524200-98544200	Strong transcription	HSMM	muscle
6	chr3:98525600-98552400	Weak transcription	Right Ventricle	heart
7	chr3:98526400-98544200	Weak transcription	Brain Angular Gyrus	brain
8	chr3:98526400-98545000	Weak transcription	Psoas Muscle	Psoas
9	chr3:98527200-98545200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr3:98527200-98545600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:98528200-98575400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr3:98528600-98543600	Strong transcription	NHEK	skin
13	chr3:98528600-98562000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr3:98529400-98546200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:98532400-98546200	Weak transcription	Esophagus	oesophagus
16	chr3:98534000-98545000	Weak transcription	Ovary	ovary
17	chr3:98534000-98552400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:98534200-98552200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:98534400-98545600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:98534600-98544200	Strong transcription	HMEC	breast
21	chr3:98534600-98545600	Weak transcription	Fetal Intestine Small	intestine
22	chr3:98535400-98543800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:98536000-98552600	Weak transcription	Pancreas	Pancrea
24	chr3:98536200-98594200	Weak transcription	HepG2	liver
25	chr3:98536800-98545000	Weak transcription	Fetal Kidney	kidney
26	chr3:98537000-98545600	Weak transcription	HSMMtube	muscle
27	chr3:98537000-98546200	Weak transcription	Brain Anterior Caudate	brain
28	chr3:98537000-98567000	Weak transcription	Stomach Smooth Muscle	stomach
29	chr3:98537000-98592800	Weak transcription	K562	blood
30	chr3:98537400-98551200	Weak transcription	Fetal Heart	heart
31	chr3:98538200-98569200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr3:98538600-98544800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:98538600-98545000	Weak transcription	Fetal Lung	lung
34	chr3:98538800-98543400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:98538800-98545400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr3:98538800-98548200	Weak transcription	Adipose Nuclei	Adipose
37	chr3:98538800-98552200	Weak transcription	Left Ventricle	heart
38	chr3:98539000-98544400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:98539400-98546400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:98540200-98543800	Strong transcription	A549	lung
41	chr3:98540200-98545000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:98540600-98543400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr3:98541200-98545000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr3:98541200-98545200	Weak transcription	Fetal Muscle Leg	muscle
45	chr3:98541200-98552200	Weak transcription	Fetal Muscle Trunk	muscle
46	chr3:98541200-98567000	Weak transcription	Liver	Liver
47	chr3:98541400-98565000	Weak transcription	HUVEC	blood vessel
48	chr3:98541600-98543400	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr3:98541600-98548400	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr3:98541800-98545600	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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