Variant report

Variant	rs6788689
Chromosome Location	chr3:98532282-98532283
allele	A/G
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	FOXA1	chr3:98531561-98532392	HepG2	liver:	n/a	n/a
2	FOXA2	chr3:98531584-98532407	A549	lung:	n/a	n/a
3	TCF12	chr3:98531630-98532489	A549	lung:	n/a	n/a
4	CEBPB	chr3:98532004-98532312	IMR90	lung:	n/a	chr3:98532156-98532167
5	CEBPB	chr3:98531907-98532328	HepG2	liver:	n/a	chr3:98532156-98532167
6	CEBPB	chr3:98531902-98532328	HepG2	liver:	n/a	chr3:98532156-98532167
7	CEBPB	chr3:98531885-98532332	A549	lung:	n/a	chr3:98532156-98532167
8	TEAD4	chr3:98531633-98532359	HepG2	liver:	n/a	n/a
9	CEBPB	chr3:98531891-98532334	MCF-7	breast:	n/a	chr3:98532156-98532167
10	CTCF	chr3:98531490-98533031	A549	lung:	n/a	n/a
11	SP1	chr3:98531826-98532371	A549	lung:	n/a	n/a
12	SP1	chr3:98531632-98532420	A549	lung:	n/a	n/a
13	FOXA2	chr3:98531727-98532447	A549	lung:	n/a	n/a
14	JUND	chr3:98531944-98532352	A549	lung:	n/a	n/a
15	EP300	chr3:98531649-98532364	A549	lung:	n/a	n/a
16	FOSL2	chr3:98531671-98532296	A549	lung:	n/a	n/a
17	NR3C1	chr3:98531826-98532294	A549	lung:	n/a	n/a
18	MBD4	chr3:98531884-98532287	HepG2	liver:	n/a	n/a
19	POLR2A	chr3:98531678-98540691	U87	brain:	n/a	n/a
20	POLR2A	chr3:98531681-98532409	U87	brain:	n/a	n/a
21	EP300	chr3:98531683-98532383	A549	lung:	n/a	n/a
22	FOXA1	chr3:98531832-98532347	HepG2	liver:	n/a	n/a
23	CTCF	chr3:98532220-98532370	GM12871	blood:	n/a	n/a
24	CEBPB	chr3:98531777-98532348	A549	lung:	n/a	chr3:98532156-98532167
25	ETS1	chr3:98531885-98532286	A549	lung:	n/a	n/a
26	POLR2A	chr3:98530977-98539024	U87	brain:	n/a	n/a
27	MAX	chr3:98531780-98532348	A549	lung:	n/a	n/a
28	POLR2A	chr3:98530971-98537862	U87	brain:	n/a	n/a
29	CEBPD	chr3:98531961-98532289	HepG2	liver:	n/a	n/a
30	CEBPB	chr3:98531724-98532407	A549	lung:	n/a	chr3:98532156-98532167
31	FOXA1	chr3:98531569-98532387	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:98311356..98313726-chr3:98530079..98532585,2	MCF-7	breast:
2	chr3:98320682..98321287-chr3:98531748..98532391,2	MCF-7	breast:

Variant related genes	Relation type
DCBLD2	TF binding region
ENSG00000080819	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1062196	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12107050	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12330170	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12490832	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13060012	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs14310	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1440150	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17270593	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1837500	0.81[ASN][1000 genomes]
rs1866677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866679	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1875086	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2028393	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2119187	0.85[ASN][1000 genomes]
rs2119188	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2262597	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2290067	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2439213	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2439214	0.87[ASN][1000 genomes]
rs2439215	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2439217	0.88[ASN][1000 genomes]
rs2439218	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2439220	0.85[ASN][1000 genomes]
rs2439222	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2439223	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2439225	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2439226	0.81[ASN][1000 genomes]
rs2439228	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2439229	0.93[ASN][1000 genomes]
rs2439231	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2439236	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2454673	0.81[ASN][1000 genomes]
rs2454676	0.88[ASN][1000 genomes]
rs2454677	0.89[ASN][1000 genomes]
rs2454678	0.88[ASN][1000 genomes]
rs2454680	0.83[ASN][1000 genomes]
rs2454682	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2454684	0.85[ASN][1000 genomes]
rs2454685	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2470857	0.85[ASN][1000 genomes]
rs2470859	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2470860	0.85[ASN][1000 genomes]
rs2470861	0.85[ASN][1000 genomes]
rs2470864	0.88[ASN][1000 genomes]
rs2470865	0.87[ASN][1000 genomes]
rs2470867	0.93[ASN][1000 genomes]
rs2470869	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2470879	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2470881	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28802000	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2919236	0.93[ASN][1000 genomes]
rs2960190	0.80[EUR][1000 genomes]
rs34234373	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34558202	1.00[ASN][1000 genomes]
rs3755574	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3755576	0.88[ASN][1000 genomes]
rs3772101	0.91[ASN][1000 genomes]
rs3772102	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4425200	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4425201	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4426625	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4426626	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4494869	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62278486	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6782630	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6785935	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6788418	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6790650	0.83[ASN][1000 genomes]
rs6804850	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6808116	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs704585	0.91[ASN][1000 genomes]
rs7611929	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7612036	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7616275	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7630800	0.85[ASN][1000 genomes]
rs828609	0.93[ASN][1000 genomes]
rs9289683	0.81[ASN][1000 genomes]
rs9811305	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9811449	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9811860	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9814819	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9815226	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9823430	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9845558	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9855175	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9860216	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9860264	0.82[EUR][1000 genomes]
rs9867586	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9873932	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9878392	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9881519	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9883516	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9883537	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs999147	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[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
rs6788689	ST3GAL6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98503400-98576400	Weak transcription	Gastric	stomach
2	chr3:98504600-98534800	Weak transcription	Small Intestine	intestine
3	chr3:98513600-98536600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:98513600-98539200	Weak transcription	Colonic Mucosa	Colon
5	chr3:98515600-98533400	Weak transcription	Fetal Intestine Small	intestine
6	chr3:98516800-98544000	Weak transcription	Spleen	Spleen
7	chr3:98522400-98533800	Strong transcription	Muscle Satellite Cultured Cells	--
8	chr3:98523600-98533800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:98523600-98535200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr3:98523800-98533600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:98523800-98533600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:98523800-98533800	Strong transcription	NHDF-Ad	bronchial
13	chr3:98523800-98535000	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:98523800-98543800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:98524000-98543600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:98524200-98544200	Strong transcription	HSMM	muscle
17	chr3:98525600-98552400	Weak transcription	Right Ventricle	heart
18	chr3:98526200-98543200	Weak transcription	Lung	lung
19	chr3:98526400-98533600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:98526400-98535600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr3:98526400-98536000	Weak transcription	Aorta	Aorta
22	chr3:98526400-98538200	Weak transcription	GM12878-XiMat	blood
23	chr3:98526400-98539200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr3:98526400-98539400	Weak transcription	Fetal Brain Male	brain
25	chr3:98526400-98542800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr3:98526400-98544200	Weak transcription	Brain Angular Gyrus	brain
27	chr3:98526400-98545000	Weak transcription	Psoas Muscle	Psoas
28	chr3:98526600-98533800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:98526600-98537400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr3:98526600-98539000	Weak transcription	Colon Smooth Muscle	Colon
31	chr3:98526600-98540000	Weak transcription	Fetal Thymus	thymus
32	chr3:98526800-98533000	Weak transcription	Duodenum Mucosa	Duodenum
33	chr3:98527000-98533800	Strong transcription	Osteobl	bone
34	chr3:98527000-98535600	Weak transcription	Pancreas	Pancrea
35	chr3:98527000-98536600	Weak transcription	Stomach Smooth Muscle	stomach
36	chr3:98527000-98536600	Weak transcription	K562	blood
37	chr3:98527000-98538600	Weak transcription	Primary T cells from cord blood	blood
38	chr3:98527200-98532400	Weak transcription	Ovary	ovary
39	chr3:98527200-98536600	Weak transcription	Brain Anterior Caudate	brain
40	chr3:98527200-98536600	Weak transcription	Brain Germinal Matrix	brain
41	chr3:98527200-98542200	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr3:98527200-98545200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr3:98527200-98545600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:98527600-98533800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:98528200-98533400	Weak transcription	Fetal Intestine Large	intestine
46	chr3:98528200-98575400	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr3:98528400-98534200	Strong transcription	HMEC	breast
48	chr3:98528400-98542200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:98528600-98533600	Weak transcription	Left Ventricle	heart
50	chr3:98528600-98533800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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