Variant report

Variant	rs1875086
Chromosome Location	chr3:98618383-98618384
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	POLR2A	chr3:98618321-98620638	SK-N-SH	brain:	n/a	n/a
2	BCL3	chr3:98618365-98619205	A549	lung:	n/a	n/a
3	MAX	chr3:98618295-98619513	A549	lung:	n/a	n/a
4	POLR2A	chr3:98618257-98622361	U87	brain:	n/a	n/a
5	POLR2A	chr3:98618207-98618796	HCT-116	colon:	n/a	n/a
6	POLR2A	chr3:98618299-98622361	U87	brain:	n/a	n/a
7	POLR2A	chr3:98618341-98621471	ProgFib	skin:	n/a	n/a
8	POLR2A	chr3:98618148-98622423	U87	brain:	n/a	n/a
9	SIN3AK20	chr3:98618244-98618723	A549	lung:	n/a	n/a
10	REST	chr3:98618368-98619272	A549	lung:	n/a	n/a
11	TAF1	chr3:98617981-98618799	A549	lung:	n/a	n/a
12	SIN3AK20	chr3:98618345-98619139	A549	lung:	n/a	n/a
13	POLR2A	chr3:98618120-98622417	U87	brain:	n/a	n/a
14	CHD1	chr3:98618292-98622396	IMR90	lung:	n/a	chr3:98620361-98620371
15	TCF12	chr3:98618229-98622320	A549	lung:	n/a	n/a
16	POLR2A	chr3:98615281-98622405	HCT-116	colon:	n/a	n/a

Variant related genes	Relation type
DCBLD2	TF binding region
ENSG00000239462	TF binding region

Extended variants
information (count: 118 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs1123293	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12054181	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1383905	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs14310	0.82[EUR][1000 genomes]
rs1440150	0.81[ASN][1000 genomes]
rs1481634	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1481635	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1481636	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1481637	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1837500	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1866677	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1866678	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1866679	0.83[EUR][1000 genomes]
rs1967009	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2028393	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2119187	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2119188	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2128051	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2128054	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2246861	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2249740	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2262597	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2290067	0.82[EUR][1000 genomes]
rs2439213	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2439214	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2439215	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2439217	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2439218	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2439220	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2439222	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439224	0.81[ASN][1000 genomes]
rs2439225	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439226	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2439228	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2439229	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2439231	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2439236	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2449001	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2449039	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2449040	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2449041	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2449042	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2454673	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2454676	0.90[ASN][1000 genomes]
rs2454677	0.91[ASN][1000 genomes]
rs2454678	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2454680	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2454682	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2454684	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2454685	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2454686	0.88[AFR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2454691	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2470821	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2470822	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2470823	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2470824	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2470825	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2470826	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2470845	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2470851	0.86[ASN][1000 genomes]
rs2470857	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2470859	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2470860	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2470861	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2470864	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2470865	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2470867	0.87[ASN][1000 genomes]
rs2470869	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2470876	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2470879	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2470881	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2470885	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs28608112	0.83[ASN][1000 genomes]
rs28802000	0.81[ASN][1000 genomes]
rs2919236	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2929490	0.83[EUR][1000 genomes]
rs2960190	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34234373	0.81[ASN][1000 genomes]
rs34558202	0.81[ASN][1000 genomes]
rs4425200	0.82[EUR][1000 genomes]
rs4426625	0.82[EUR][1000 genomes]
rs4450736	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62276887	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6440280	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6782630	0.82[EUR][1000 genomes]
rs6785935	0.81[ASN][1000 genomes]
rs6788418	0.81[ASN][1000 genomes]
rs6788689	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6804850	0.82[EUR][1000 genomes]
rs7616275	0.81[ASN][1000 genomes]
rs7630800	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7631624	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9289683	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9289685	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9811449	0.81[EUR][1000 genomes]
rs9811860	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9814819	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9815226	0.82[EUR][1000 genomes]
rs9820384	0.81[ASN][1000 genomes]
rs9823430	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9835142	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9843864	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9845558	0.81[ASN][1000 genomes]
rs9849048	0.81[ASN][1000 genomes]
rs9852950	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9860216	0.81[ASN][1000 genomes]
rs9860264	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9867586	0.84[EUR][1000 genomes]
rs9873932	0.81[ASN][1000 genomes]
rs9883516	0.81[EUR][1000 genomes]
rs9883537	0.81[EUR][1000 genomes]
rs999147	0.82[EUR][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	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
2	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
3	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
4	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
5	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1875086	ST3GAL6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98593800-98619400	Weak transcription	Small Intestine	intestine
2	chr3:98597400-98619000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr3:98599800-98618400	Weak transcription	Fetal Brain Female	brain
4	chr3:98605000-98618600	Weak transcription	Fetal Stomach	stomach
5	chr3:98606400-98618400	Weak transcription	Fetal Kidney	kidney
6	chr3:98610800-98618400	Weak transcription	Brain Anterior Caudate	brain
7	chr3:98610800-98618400	Enhancers	Fetal Heart	heart
8	chr3:98610800-98618600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr3:98611400-98618800	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr3:98611400-98619200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr3:98611800-98618400	Weak transcription	Colon Smooth Muscle	Colon
12	chr3:98611800-98618600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr3:98612000-98618800	Weak transcription	Psoas Muscle	Psoas
14	chr3:98612600-98618400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:98612800-98618400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:98613000-98618400	Weak transcription	GM12878-XiMat	blood
17	chr3:98613000-98618600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr3:98613000-98618600	Weak transcription	Fetal Muscle Leg	muscle
19	chr3:98613000-98618600	Weak transcription	HSMMtube	muscle
20	chr3:98613200-98618600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr3:98613200-98618800	Weak transcription	Brain Hippocampus Middle	brain
22	chr3:98613200-98619200	Weak transcription	Aorta	Aorta
23	chr3:98613200-98619400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr3:98613400-98618400	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr3:98613600-98619400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr3:98614200-98619600	Weak transcription	Gastric	stomach
27	chr3:98614400-98618400	Weak transcription	Brain Germinal Matrix	brain
28	chr3:98614400-98618400	Weak transcription	Right Atrium	heart
29	chr3:98614400-98618600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr3:98614400-98619000	Weak transcription	K562	blood
31	chr3:98614600-98618400	Weak transcription	Ovary	ovary
32	chr3:98615000-98618400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:98615000-98619400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr3:98615000-98620400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:98615200-98618600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr3:98615600-98619600	Flanking Active TSS	HUVEC	blood vessel
37	chr3:98615600-98621200	Active TSS	NHLF	lung
38	chr3:98616000-98618400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr3:98616000-98618600	Active TSS	HMEC	breast
40	chr3:98616400-98618400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr3:98616400-98618400	Active TSS	NHEK	skin
42	chr3:98616600-98618600	Enhancers	Dnd41	blood
43	chr3:98616600-98618800	Active TSS	Muscle Satellite Cultured Cells	--
44	chr3:98616600-98621400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:98616800-98621200	Active TSS	NHDF-Ad	bronchial
46	chr3:98617000-98618400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:98617200-98618400	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr3:98617400-98618400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr3:98617400-98618400	Active TSS	HSMM	muscle
50	chr3:98617400-98618600	Enhancers	iPS-15b Cell Line	embryonic stem cell

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