Variant report

Variant	rs3772099
Chromosome Location	chr3:98492380-98492381
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1062196	0.96[CEU][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12107050	1.00[CEU][hapmap];0.85[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12330170	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12490832	1.00[CEU][hapmap];0.85[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13060012	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs14310	0.85[JPT][hapmap]
rs1440150	1.00[CEU][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1440151	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1440152	0.89[CEU][hapmap];0.92[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17270593	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1837500	0.96[CEU][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs1866677	0.85[JPT][hapmap]
rs1866678	0.85[JPT][hapmap]
rs2119187	1.00[CEU][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes]
rs2119188	0.84[JPT][hapmap]
rs2279761	0.82[EUR][1000 genomes]
rs2290067	0.84[JPT][hapmap]
rs2334230	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439214	0.87[EUR][1000 genomes]
rs2439217	0.88[EUR][1000 genomes]
rs2439220	0.84[EUR][1000 genomes]
rs2439222	0.84[JPT][hapmap]
rs2439223	0.85[JPT][hapmap]
rs2439226	0.84[EUR][1000 genomes]
rs2439229	0.92[EUR][1000 genomes]
rs2439231	0.85[JPT][hapmap]
rs2439236	0.85[JPT][hapmap]
rs2454673	0.96[CEU][hapmap];0.84[JPT][hapmap];0.83[EUR][1000 genomes]
rs2454676	0.91[EUR][1000 genomes]
rs2454677	0.90[EUR][1000 genomes]
rs2454678	0.84[EUR][1000 genomes]
rs2454680	0.84[EUR][1000 genomes]
rs2454682	0.84[JPT][hapmap]
rs2454684	0.87[EUR][1000 genomes]
rs2454685	0.84[JPT][hapmap]
rs2454691	0.83[EUR][1000 genomes]
rs2470857	1.00[CEU][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes]
rs2470859	0.85[JPT][hapmap]
rs2470860	0.86[EUR][1000 genomes]
rs2470861	0.96[CEU][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs2470864	0.92[EUR][1000 genomes]
rs2470865	0.92[EUR][1000 genomes]
rs2470867	1.00[CEU][hapmap];0.84[JPT][hapmap];0.91[EUR][1000 genomes]
rs2470869	0.84[JPT][hapmap]
rs2470881	0.85[JPT][hapmap]
rs2470885	0.96[CEU][hapmap];0.84[JPT][hapmap];0.83[EUR][1000 genomes]
rs28802000	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2919234	0.90[EUR][1000 genomes]
rs2919236	0.92[EUR][1000 genomes]
rs34234373	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34558202	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3755574	0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3755576	1.00[CEU][hapmap];0.84[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3772098	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3772101	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3772102	1.00[CEU][hapmap];0.85[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3821359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4269027	0.80[EUR][1000 genomes]
rs4425200	0.84[JPT][hapmap];0.80[AMR][1000 genomes]
rs4425201	1.00[CEU][hapmap];0.84[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4426625	0.85[JPT][hapmap];0.80[AMR][1000 genomes]
rs4426626	1.00[CEU][hapmap];0.85[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4494869	1.00[CEU][hapmap];0.85[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62278486	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6782630	0.85[JPT][hapmap]
rs6785935	1.00[CEU][hapmap];0.84[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6788418	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6790650	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6804850	0.85[JPT][hapmap]
rs6808116	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs704585	1.00[CEU][hapmap];0.84[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7431448	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7611929	1.00[CEU][hapmap];0.85[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7612036	1.00[CEU][hapmap];0.85[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7612605	0.91[EUR][1000 genomes]
rs7616275	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7630800	0.84[EUR][1000 genomes]
rs828609	1.00[CEU][hapmap];0.84[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs844160	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9289683	1.00[CEU][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes]
rs9289685	0.83[EUR][1000 genomes]
rs9811305	1.00[CEU][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9811449	0.85[JPT][hapmap];0.80[AMR][1000 genomes]
rs9811860	0.85[JPT][hapmap]
rs9814819	0.85[JPT][hapmap]
rs9815226	0.85[JPT][hapmap];0.80[AMR][1000 genomes]
rs9820384	0.84[EUR][1000 genomes]
rs9823430	0.85[JPT][hapmap]
rs9843214	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs9845558	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9860216	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9866570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9872152	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9873932	1.00[CEU][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9878392	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9881519	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9883516	0.85[JPT][hapmap];0.81[AMR][1000 genomes]
rs9883537	0.84[JPT][hapmap];0.80[AMR][1000 genomes]
rs999147	0.84[JPT][hapmap];0.80[AMR][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
rs3772099	ST3GAL6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:60 , 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	chr3:98482200-98495800	Weak transcription	Dnd41	blood
3	chr3:98482400-98496000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr3:98482600-98494600	Weak transcription	Aorta	Aorta
5	chr3:98482600-98501800	Weak transcription	Fetal Stomach	stomach
6	chr3:98482800-98497400	Weak transcription	Fetal Muscle Leg	muscle
7	chr3:98483000-98497400	Weak transcription	Spleen	Spleen
8	chr3:98483000-98517600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:98483200-98518000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr3:98483600-98495200	Weak transcription	Fetal Thymus	thymus
11	chr3:98483600-98513600	Weak transcription	Brain Germinal Matrix	brain
12	chr3:98483800-98496400	Weak transcription	Fetal Lung	lung
13	chr3:98483800-98515000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr3:98484000-98498000	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:98484000-98514000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr3:98484200-98515200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr3:98484800-98529800	Weak transcription	Primary B cells from cord blood	blood
18	chr3:98485000-98496200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr3:98488200-98496800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr3:98488600-98496200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr3:98488600-98497200	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr3:98488600-98497200	Weak transcription	Fetal Kidney	kidney
23	chr3:98489200-98493200	Strong transcription	HUVEC	blood vessel
24	chr3:98489600-98494400	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr3:98489600-98497000	Weak transcription	Lung	lung
26	chr3:98489800-98494000	Weak transcription	Thymus	Thymus
27	chr3:98489800-98494600	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr3:98489800-98494600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr3:98489800-98495200	Weak transcription	Pancreas	Pancrea
30	chr3:98489800-98495800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr3:98489800-98496000	Weak transcription	Stomach Mucosa	stomach
32	chr3:98489800-98496200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr3:98489800-98496400	Weak transcription	Placenta	Placenta
34	chr3:98489800-98496600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:98489800-98496600	Weak transcription	Adipose Nuclei	Adipose
36	chr3:98489800-98497000	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr3:98489800-98497400	Weak transcription	Right Ventricle	heart
38	chr3:98489800-98497600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr3:98489800-98503000	Weak transcription	Psoas Muscle	Psoas
40	chr3:98490000-98494400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr3:98490000-98495800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr3:98490000-98496200	Weak transcription	Brain Substantia Nigra	brain
43	chr3:98490000-98496400	Weak transcription	Brain Anterior Caudate	brain
44	chr3:98490200-98494000	Weak transcription	GM12878-XiMat	blood
45	chr3:98490200-98494400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:98490200-98494400	Weak transcription	Fetal Heart	heart
47	chr3:98490200-98496000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:98490200-98496000	Weak transcription	Brain Angular Gyrus	brain
49	chr3:98490200-98496400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr3:98490200-98525200	Weak transcription	Rectal Smooth Muscle	rectum

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