Variant report

Variant	rs6790650
Chromosome Location	chr3:98499779-98499780
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:98499347-98499843	U87	brain:	n/a	n/a
2	POLR2A	chr3:98499303-98499843	U87	brain:	n/a	n/a
3	POLR2A	chr3:98498651-98499815	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
PDLIM1P4	TF binding region
ST3GAL6	TF binding region

Extended variants
information (count: 95 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1062196	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12107050	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12330170	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12490832	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13060012	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs14310	0.87[ASN][1000 genomes]
rs1440150	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1440151	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1440152	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17270593	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1837500	0.83[EUR][1000 genomes]
rs1866677	0.83[ASN][1000 genomes]
rs1866678	0.83[ASN][1000 genomes]
rs1866679	0.85[ASN][1000 genomes]
rs2119187	0.84[EUR][1000 genomes]
rs2279761	0.82[EUR][1000 genomes]
rs2290067	0.89[ASN][1000 genomes]
rs2334230	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2439214	0.86[EUR][1000 genomes]
rs2439217	0.86[EUR][1000 genomes]
rs2439220	0.84[EUR][1000 genomes]
rs2439226	0.85[EUR][1000 genomes]
rs2439229	0.90[EUR][1000 genomes]
rs2454673	0.83[EUR][1000 genomes]
rs2454676	0.89[EUR][1000 genomes]
rs2454677	0.88[EUR][1000 genomes]
rs2454678	0.82[EUR][1000 genomes]
rs2454680	0.85[EUR][1000 genomes]
rs2454684	0.87[EUR][1000 genomes]
rs2454691	0.83[EUR][1000 genomes]
rs2470857	0.85[EUR][1000 genomes]
rs2470860	0.86[EUR][1000 genomes]
rs2470861	0.85[EUR][1000 genomes]
rs2470864	0.90[EUR][1000 genomes]
rs2470865	0.90[EUR][1000 genomes]
rs2470867	0.89[EUR][1000 genomes]
rs2470885	0.83[EUR][1000 genomes]
rs28802000	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2919234	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2919236	0.90[EUR][1000 genomes]
rs34234373	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34558202	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3755574	0.90[ASN][1000 genomes]
rs3755576	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3772098	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3772099	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3772101	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3772102	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3821359	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4425200	0.89[ASN][1000 genomes]
rs4425201	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4426625	0.89[ASN][1000 genomes]
rs4426626	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4494869	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62278486	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6782630	0.87[ASN][1000 genomes]
rs6785935	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6788418	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6788689	0.83[ASN][1000 genomes]
rs6804850	0.89[ASN][1000 genomes]
rs6808116	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs704585	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7431448	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7611929	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7612036	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7612605	0.89[EUR][1000 genomes]
rs7616275	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7630800	0.85[EUR][1000 genomes]
rs828609	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs844160	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9289683	0.85[EUR][1000 genomes]
rs9289685	0.83[EUR][1000 genomes]
rs9811305	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9811449	0.91[ASN][1000 genomes]
rs9811860	0.83[ASN][1000 genomes]
rs9814819	0.83[ASN][1000 genomes]
rs9815226	0.91[ASN][1000 genomes]
rs9820384	0.85[EUR][1000 genomes]
rs9823430	0.83[ASN][1000 genomes]
rs9845558	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9855175	0.91[ASN][1000 genomes]
rs9860216	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9866570	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9872152	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9873932	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9878392	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9881519	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9883516	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9883537	0.89[ASN][1000 genomes]
rs999147	0.89[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
rs6790650	ST3GAL6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:76 , 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	chr3:98482600-98501800	Weak transcription	Fetal Stomach	stomach
3	chr3:98483000-98517600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:98483200-98518000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:98483600-98513600	Weak transcription	Brain Germinal Matrix	brain
6	chr3:98483800-98515000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr3:98484000-98514000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr3:98484200-98515200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr3:98484800-98529800	Weak transcription	Primary B cells from cord blood	blood
10	chr3:98489800-98503000	Weak transcription	Psoas Muscle	Psoas
11	chr3:98490200-98525200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:98492200-98517800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:98494600-98506000	Enhancers	Aorta	Aorta
14	chr3:98496000-98499800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:98496000-98499800	Enhancers	NH-A	brain
16	chr3:98496200-98499800	Enhancers	Brain Substantia Nigra	brain
17	chr3:98496400-98499800	Enhancers	Brain Anterior Caudate	brain
18	chr3:98496600-98503800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:98496800-98502800	Weak transcription	Fetal Thymus	thymus
20	chr3:98497000-98524600	Weak transcription	Fetal Brain Male	brain
21	chr3:98497400-98499800	Strong transcription	Dnd41	blood
22	chr3:98497400-98501800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:98497400-98503600	Enhancers	Placenta	Placenta
24	chr3:98497600-98499800	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr3:98497600-98502400	Weak transcription	Lung	lung
26	chr3:98497800-98517200	Weak transcription	Fetal Brain Female	brain
27	chr3:98498000-98499800	Enhancers	HMEC	breast
28	chr3:98498000-98500400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr3:98498000-98500400	Weak transcription	Pancreas	Pancrea
30	chr3:98498000-98501800	Weak transcription	Gastric	stomach
31	chr3:98498000-98503000	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr3:98498000-98516600	Weak transcription	Stomach Mucosa	stomach
33	chr3:98498200-98505400	Strong transcription	Thymus	Thymus
34	chr3:98498400-98499800	Genic enhancers	HepG2	liver
35	chr3:98498400-98500000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:98498400-98501600	Weak transcription	GM12878-XiMat	blood
37	chr3:98498400-98504600	Weak transcription	Fetal Intestine Small	intestine
38	chr3:98498600-98499800	Strong transcription	Primary hematopoietic stem cells	blood
39	chr3:98498600-98499800	Enhancers	Osteobl	bone
40	chr3:98498600-98500000	Strong transcription	Liver	Liver
41	chr3:98498600-98503000	Weak transcription	Right Atrium	heart
42	chr3:98498800-98500600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr3:98498800-98502000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr3:98498800-98506800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr3:98498800-98512800	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr3:98499000-98499800	Flanking Active TSS	HUVEC	blood vessel
47	chr3:98499000-98503000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:98499000-98503000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr3:98499000-98504200	Weak transcription	HSMM	muscle
50	chr3:98499200-98500400	Weak transcription	Right Ventricle	heart

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