Variant report

Variant	rs62278486
Chromosome Location	chr3:98503941-98503942
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:98502998..98505782-chr3:98508615..98511357,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000064225	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1062196	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12107050	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12330170	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12490832	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13060012	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs14310	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1440150	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1440151	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1440152	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17270593	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1837500	0.84[EUR][1000 genomes]
rs1866677	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1866678	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1866679	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2119187	0.85[EUR][1000 genomes]
rs2262597	0.83[ASN][1000 genomes]
rs2279761	0.83[EUR][1000 genomes]
rs2290067	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2334230	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2439213	0.82[ASN][1000 genomes]
rs2439214	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2439215	0.83[ASN][1000 genomes]
rs2439217	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2439218	0.83[ASN][1000 genomes]
rs2439220	0.85[EUR][1000 genomes]
rs2439226	0.86[EUR][1000 genomes]
rs2439228	0.86[ASN][1000 genomes]
rs2439229	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2439231	0.87[ASN][1000 genomes]
rs2439236	0.83[ASN][1000 genomes]
rs2454673	0.84[EUR][1000 genomes]
rs2454676	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2454677	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2454678	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2454680	0.86[EUR][1000 genomes]
rs2454684	0.89[EUR][1000 genomes]
rs2454691	0.83[EUR][1000 genomes]
rs2470857	0.86[EUR][1000 genomes]
rs2470860	0.88[EUR][1000 genomes]
rs2470861	0.86[EUR][1000 genomes]
rs2470864	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2470865	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2470867	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2470869	0.87[ASN][1000 genomes]
rs2470879	0.87[ASN][1000 genomes]
rs2470885	0.83[EUR][1000 genomes]
rs28802000	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2919234	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2919236	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34234373	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34558202	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3755574	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3755576	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3772098	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3772099	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3772101	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3772102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3821359	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4269027	0.82[EUR][1000 genomes]
rs4425200	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4425201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4426625	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4426626	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4494869	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782630	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6785935	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6788418	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6788689	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6790650	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6804850	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6808116	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs704585	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7431448	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7611929	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7612036	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7612605	0.92[EUR][1000 genomes]
rs7616275	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7630800	0.86[EUR][1000 genomes]
rs828609	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs844160	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9289683	0.86[EUR][1000 genomes]
rs9289685	0.83[EUR][1000 genomes]
rs9811305	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9811449	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9811860	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9814819	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9815226	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9820384	0.86[EUR][1000 genomes]
rs9823430	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9845558	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9855175	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9860216	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9866570	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9867586	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9872152	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9873932	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9878392	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9881519	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9883516	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9883537	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs999147	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62278486	ST3GAL6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98478800-98515200	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr3:98483000-98517600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:98483200-98518000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr3:98483600-98513600	Weak transcription	Brain Germinal Matrix	brain
5	chr3:98483800-98515000	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr3:98484000-98514000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:98484200-98515200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr3:98484800-98529800	Weak transcription	Primary B cells from cord blood	blood
9	chr3:98490200-98525200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:98492200-98517800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:98494600-98506000	Enhancers	Aorta	Aorta
12	chr3:98497000-98524600	Weak transcription	Fetal Brain Male	brain
13	chr3:98497800-98517200	Weak transcription	Fetal Brain Female	brain
14	chr3:98498000-98516600	Weak transcription	Stomach Mucosa	stomach
15	chr3:98498200-98505400	Strong transcription	Thymus	Thymus
16	chr3:98498400-98504600	Weak transcription	Fetal Intestine Small	intestine
17	chr3:98498800-98506800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:98498800-98512800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr3:98499000-98504200	Weak transcription	HSMM	muscle
20	chr3:98499200-98504200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr3:98499200-98504600	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr3:98499200-98516600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr3:98499400-98506400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:98499600-98507800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:98499600-98516600	Weak transcription	Brain Angular Gyrus	brain
26	chr3:98499800-98514800	Weak transcription	Dnd41	blood
27	chr3:98500200-98506000	Enhancers	HMEC	breast
28	chr3:98500600-98504400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:98500800-98505600	Genic enhancers	Monocytes-CD14+_RO01746	blood
30	chr3:98501000-98506600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:98501000-98507400	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr3:98501200-98504400	Weak transcription	Brain Hippocampus Middle	brain
33	chr3:98501200-98513400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr3:98501400-98505800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr3:98501400-98506000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:98501400-98506000	Enhancers	NH-A	brain
37	chr3:98501800-98504200	Enhancers	Liver	Liver
38	chr3:98501800-98504800	Enhancers	NHEK	skin
39	chr3:98502000-98506000	Enhancers	Muscle Satellite Cultured Cells	--
40	chr3:98502200-98505000	Enhancers	HepG2	liver
41	chr3:98502200-98506200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr3:98502200-98506600	Genic enhancers	Primary monocytes fromperipheralblood	blood
43	chr3:98502200-98519800	Weak transcription	Fetal Kidney	kidney
44	chr3:98502200-98523800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:98502400-98504800	Weak transcription	GM12878-XiMat	blood
46	chr3:98502400-98523800	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr3:98502600-98505800	Weak transcription	Fetal Intestine Large	intestine
48	chr3:98502600-98513400	Weak transcription	Fetal Stomach	stomach
49	chr3:98502800-98505200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr3:98502800-98505400	Strong transcription	Fetal Thymus	thymus

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