Variant report

Variant	rs13060012
Chromosome Location	chr3:98502147-98502148
allele	A/C
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	MYBL2	chr3:98501920-98502395	HepG2	liver:	n/a	n/a
2	NR3C1	chr3:98501957-98502357	A549	lung:	n/a	chr3:98502287-98502303 chr3:98502287-98502303 chr3:98502209-98502218
3	EP300	chr3:98501684-98502378	HepG2	liver:	n/a	chr3:98502310-98502324
4	ARID3A	chr3:98502008-98502371	HepG2	liver:	n/a	n/a
5	HNF4A	chr3:98502051-98502357	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:98500239-98520630	U87	brain:	n/a	n/a
7	NFATC1	chr3:98501901-98502355	GM12878	blood:	n/a	n/a
8	HDAC2	chr3:98501982-98502439	HepG2	liver:	n/a	n/a
9	EP300	chr3:98502049-98502334	HepG2	liver:	n/a	chr3:98502310-98502324
10	FOXM1	chr3:98501972-98502353	GM12878	blood:	n/a	n/a
11	SMC3	chr3:98502114-98502379	HepG2	liver:	n/a	n/a
12	JUND	chr3:98501898-98502367	HepG2	liver:	n/a	chr3:98502209-98502217 chr3:98502207-98502218 chr3:98502210-98502221
13	TEAD4	chr3:98501990-98502393	HepG2	liver:	n/a	n/a
14	CHD2	chr3:98502019-98502295	HepG2	liver:	n/a	n/a
15	RAD21	chr3:98501857-98502374	HepG2	liver:	n/a	n/a
16	NR3C1	chr3:98501982-98502410	ECC-1	luminal epithelium:	n/a	chr3:98502287-98502303 chr3:98502287-98502303 chr3:98502209-98502218
17	MBD4	chr3:98502080-98502389	HepG2	liver:	n/a	n/a
18	HEY1	chr3:98501947-98502167	HepG2	liver:	n/a	n/a
19	PAX5	chr3:98502015-98502337	GM12878	blood:	n/a	n/a
20	SP1	chr3:98501966-98502353	HepG2	liver:	n/a	n/a
21	FOXA2	chr3:98502052-98502382	HepG2	liver:	n/a	n/a
22	PAX5	chr3:98502010-98502275	GM12878	blood:	n/a	n/a
23	HNF4G	chr3:98501953-98502385	HepG2	liver:	n/a	chr3:98502180-98502195
24	FOSL2	chr3:98501933-98502362	HepG2	liver:	n/a	chr3:98502209-98502217 chr3:98502210-98502221
25	HNF4A	chr3:98501982-98502409	HepG2	liver:	n/a	n/a
26	POLR2A	chr3:98501921-98502297	HepG2	liver:	n/a	n/a
27	HDAC2	chr3:98502000-98502388	HepG2	liver:	n/a	n/a
28	POLR2A	chr3:98500581-98518912	U87	brain:	n/a	n/a
29	NR3C1	chr3:98501741-98502431	ECC-1	luminal epithelium:	n/a	chr3:98502287-98502303 chr3:98502287-98502303 chr3:98502209-98502218
30	EP300	chr3:98501557-98502433	ECC-1	luminal epithelium:	n/a	chr3:98502310-98502324
31	EP300	chr3:98502089-98502455	HepG2	liver:	n/a	chr3:98502310-98502324
32	RUNX3	chr3:98502050-98502363	GM12878	blood:	n/a	n/a
33	NFIC	chr3:98501958-98502400	HepG2	liver:	n/a	n/a
34	RUNX3	chr3:98501890-98502394	GM12878	blood:	n/a	n/a
35	POLR2A	chr3:98500433-98518912	U87	brain:	n/a	n/a
36	TBP	chr3:98501968-98502278	HepG2	liver:	n/a	n/a
37	TCF12	chr3:98501738-98502403	ECC-1	luminal epithelium:	n/a	n/a
38	NFIC	chr3:98501994-98502403	GM12878	blood:	n/a	n/a
39	MXI1	chr3:98502067-98502378	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ST3GAL6	TF binding region

Extended variants
information (count: 105 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs1062196	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12107050	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12330170	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12490832	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs14310	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1440150	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[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];1.00[ASN][1000 genomes]
rs1837500	0.84[EUR][1000 genomes]
rs1866677	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1866678	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1866679	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2119187	0.85[EUR][1000 genomes]
rs2262597	0.81[ASN][1000 genomes]
rs2279761	0.83[EUR][1000 genomes]
rs2290067	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2334230	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2439214	0.89[EUR][1000 genomes]
rs2439215	0.81[ASN][1000 genomes]
rs2439217	0.90[EUR][1000 genomes]
rs2439218	0.81[ASN][1000 genomes]
rs2439220	0.85[EUR][1000 genomes]
rs2439226	0.86[EUR][1000 genomes]
rs2439228	0.84[ASN][1000 genomes]
rs2439229	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2439231	0.85[ASN][1000 genomes]
rs2439236	0.81[ASN][1000 genomes]
rs2454673	0.84[EUR][1000 genomes]
rs2454676	0.93[EUR][1000 genomes]
rs2454677	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2454678	0.86[EUR][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]
rs2470865	0.93[EUR][1000 genomes]
rs2470867	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2470869	0.85[ASN][1000 genomes]
rs2470879	0.85[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];0.91[ASN][1000 genomes]
rs2919234	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2919236	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34234373	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34558202	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3755574	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3755576	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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];1.00[ASN][1000 genomes]
rs3772102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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];0.98[ASN][1000 genomes]
rs4425201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4426625	0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4426626	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4494869	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62278486	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6782630	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6785935	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6788418	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6788689	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6790650	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6804850	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6808116	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs704585	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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];0.98[ASN][1000 genomes]
rs7612036	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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];0.91[ASN][1000 genomes]
rs7630800	0.86[EUR][1000 genomes]
rs828609	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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];1.00[ASN][1000 genomes]
rs9811449	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9811860	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9814819	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9815226	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9820384	0.86[EUR][1000 genomes]
rs9823430	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9845558	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9855175	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9860216	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9866570	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9867586	0.80[AMR][1000 genomes];0.86[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];0.91[ASN][1000 genomes]
rs9878392	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881519	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9883516	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9883537	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs999147	0.86[AMR][1000 genomes];0.98[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
rs13060012	ST3GAL6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:78 , 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	chr3:98489800-98503000	Weak transcription	Psoas Muscle	Psoas
10	chr3:98490200-98525200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr3:98492200-98517800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:98494600-98506000	Enhancers	Aorta	Aorta
13	chr3:98496600-98503800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:98496800-98502800	Weak transcription	Fetal Thymus	thymus
15	chr3:98497000-98524600	Weak transcription	Fetal Brain Male	brain
16	chr3:98497400-98503600	Enhancers	Placenta	Placenta
17	chr3:98497600-98502400	Weak transcription	Lung	lung
18	chr3:98497800-98517200	Weak transcription	Fetal Brain Female	brain
19	chr3:98498000-98503000	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr3:98498000-98516600	Weak transcription	Stomach Mucosa	stomach
21	chr3:98498200-98505400	Strong transcription	Thymus	Thymus
22	chr3:98498400-98504600	Weak transcription	Fetal Intestine Small	intestine
23	chr3:98498600-98503000	Weak transcription	Right Atrium	heart
24	chr3:98498800-98506800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:98498800-98512800	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr3:98499000-98503000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:98499000-98503000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr3:98499000-98504200	Weak transcription	HSMM	muscle
29	chr3:98499200-98502200	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr3:98499200-98503200	Weak transcription	NHDF-Ad	bronchial
31	chr3:98499200-98503400	Weak transcription	NHLF	lung
32	chr3:98499200-98504200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr3:98499200-98504600	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr3:98499200-98516600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr3:98499400-98503000	Weak transcription	Fetal Heart	heart
36	chr3:98499400-98503600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr3:98499400-98506400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:98499600-98502200	Weak transcription	Brain Cingulate Gyrus	brain
39	chr3:98499600-98503000	Weak transcription	Adipose Nuclei	Adipose
40	chr3:98499600-98507800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:98499600-98516600	Weak transcription	Brain Angular Gyrus	brain
42	chr3:98499800-98502200	Weak transcription	Brain Anterior Caudate	brain
43	chr3:98499800-98502200	Weak transcription	Brain Substantia Nigra	brain
44	chr3:98499800-98502800	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr3:98499800-98503200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:98499800-98514800	Weak transcription	Dnd41	blood
47	chr3:98500200-98506000	Enhancers	HMEC	breast
48	chr3:98500400-98502400	Genic enhancers	Right Ventricle	heart
49	chr3:98500600-98502800	Strong transcription	Primary hematopoietic stem cells	blood
50	chr3:98500600-98504400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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