Variant report

Variant	rs2919234
Chromosome Location	chr3:98498238-98498239
allele	A/C/G/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	USF1	chr3:98497855-98498290	SK-N-SH	brain:	n/a	chr3:98498010-98498021
2	USF1	chr3:98497838-98498302	SK-N-SH_RA	brain:	n/a	chr3:98498010-98498021
3	MYC	chr3:98497587-98498325	MCF10A-Er-Src	breast:	n/a	chr3:98498010-98498023 chr3:98498012-98498021 chr3:98498011-98498022
4	FOS	chr3:98497286-98498328	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr3:98497629-98498357	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr3:98497655-98498431	HUVEC	blood vessel:	n/a	n/a
7	NFIC	chr3:98497552-98498458	SK-N-SH	brain:	n/a	n/a
8	MAX	chr3:98497809-98498382	HUVEC	blood vessel:	n/a	chr3:98498010-98498023 chr3:98498012-98498021 chr3:98498011-98498022
9	POLR2A	chr3:98497193-98498558	U87	brain:	n/a	n/a
10	USF1	chr3:98497807-98498288	SK-N-SH_RA	brain:	n/a	chr3:98498010-98498021
11	PBX3	chr3:98497497-98498359	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr3:98497734-98498293	HUVEC	blood vessel:	n/a	n/a
13	FOS	chr3:98497184-98498296	MCF10A-Er-Src	breast:	n/a	n/a
14	NFATC1	chr3:98497772-98498306	GM12878	blood:	n/a	n/a
15	JUND	chr3:98497623-98498292	HepG2	liver:	n/a	n/a
16	GATA2	chr3:98497735-98498392	HUVEC	blood vessel:	n/a	n/a
17	MAX	chr3:98497828-98498413	SK-N-SH	brain:	n/a	chr3:98498010-98498023 chr3:98498012-98498021 chr3:98498011-98498022
18	HNF4A	chr3:98497656-98498264	HepG2	liver:	n/a	n/a
19	POLR2A	chr3:98497865-98498333	HUVEC	blood vessel:	n/a	n/a
20	POLR2A	chr3:98496882-98498523	U87	brain:	n/a	n/a
21	FOS	chr3:98497583-98498265	MCF10A-Er-Src	breast:	n/a	n/a
22	GATA3	chr3:98497479-98498320	SK-N-SH	brain:	n/a	n/a
23	CEBPB	chr3:98497292-98498262	IMR90	lung:	n/a	chr3:98497806-98497817
24	JUN	chr3:98497685-98498443	HUVEC	blood vessel:	n/a	n/a
25	FOS	chr3:98497223-98498320	HUVEC	blood vessel:	n/a	n/a
26	USF1	chr3:98497730-98498268	HepG2	liver:	n/a	chr3:98498010-98498021
27	FOS	chr3:98497652-98498270	MCF10A-Er-Src	breast:	n/a	n/a
28	CEBPB	chr3:98497378-98498297	HepG2	liver:	n/a	chr3:98497806-98497817
29	MYC	chr3:98497555-98498334	MCF10A-Er-Src	breast:	n/a	chr3:98498010-98498023 chr3:98498012-98498021 chr3:98498011-98498022
30	MAX	chr3:98497685-98498379	SK-N-SH	brain:	n/a	chr3:98498010-98498023 chr3:98498012-98498021 chr3:98498011-98498022

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

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1062196	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12107050	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12330170	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12490832	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13060012	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs14310	0.81[ASN][1000 genomes]
rs1440150	0.87[EUR][1000 genomes]
rs1440151	0.90[EUR][1000 genomes]
rs1440152	0.89[EUR][1000 genomes]
rs17270593	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2290067	0.83[ASN][1000 genomes]
rs2334230	0.90[EUR][1000 genomes]
rs2439229	0.82[EUR][1000 genomes]
rs2454676	0.81[EUR][1000 genomes]
rs2454677	0.80[EUR][1000 genomes]
rs2470864	0.82[EUR][1000 genomes]
rs2470865	0.82[EUR][1000 genomes]
rs2470867	0.81[EUR][1000 genomes]
rs28802000	0.85[EUR][1000 genomes]
rs2919236	0.82[EUR][1000 genomes]
rs34234373	0.85[EUR][1000 genomes]
rs34558202	0.84[EUR][1000 genomes]
rs3755574	0.82[ASN][1000 genomes]
rs3755576	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3772098	0.89[EUR][1000 genomes]
rs3772099	0.90[EUR][1000 genomes]
rs3772101	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3772102	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3821359	0.89[EUR][1000 genomes]
rs4425200	0.83[ASN][1000 genomes]
rs4425201	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4426625	0.83[ASN][1000 genomes]
rs4426626	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4494869	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62278486	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6782630	0.81[ASN][1000 genomes]
rs6785935	0.87[EUR][1000 genomes]
rs6788418	0.85[EUR][1000 genomes]
rs6790650	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6804850	0.83[ASN][1000 genomes]
rs6808116	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs704585	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7431448	0.90[EUR][1000 genomes]
rs7611929	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7612036	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7612605	0.82[EUR][1000 genomes]
rs7616275	0.85[EUR][1000 genomes]
rs828609	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs844160	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9811305	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9811449	0.85[ASN][1000 genomes]
rs9815226	0.85[ASN][1000 genomes]
rs9845558	0.85[EUR][1000 genomes]
rs9855175	0.85[ASN][1000 genomes]
rs9860216	0.87[EUR][1000 genomes]
rs9866570	0.90[EUR][1000 genomes]
rs9872152	0.90[EUR][1000 genomes]
rs9873932	0.86[EUR][1000 genomes]
rs9878392	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9881519	0.86[EUR][1000 genomes]
rs9883516	0.83[ASN][1000 genomes]
rs9883537	0.83[ASN][1000 genomes]
rs999147	0.83[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
rs2919234	ST3GAL6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:79 , 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	chr3:98493800-98498400	Enhancers	HepG2	liver
14	chr3:98493800-98499600	Enhancers	Fetal Intestine Large	intestine
15	chr3:98494400-98498400	Enhancers	Fetal Intestine Small	intestine
16	chr3:98494600-98499200	Genic enhancers	Primary monocytes fromperipheralblood	blood
17	chr3:98494600-98506000	Enhancers	Aorta	Aorta
18	chr3:98495800-98499200	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr3:98495800-98499600	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr3:98496000-98499200	Enhancers	NHLF	lung
21	chr3:98496000-98499600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:98496000-98499600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:98496000-98499800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:98496000-98499800	Enhancers	NH-A	brain
25	chr3:98496200-98498600	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr3:98496200-98498800	Enhancers	Brain Hippocampus Middle	brain
27	chr3:98496200-98499000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr3:98496200-98499200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:98496200-98499400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:98496200-98499600	Enhancers	Brain Cingulate Gyrus	brain
31	chr3:98496200-98499800	Enhancers	Brain Substantia Nigra	brain
32	chr3:98496400-98498800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:98496400-98499400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:98496400-98499800	Enhancers	Brain Anterior Caudate	brain
35	chr3:98496600-98499600	Enhancers	Adipose Nuclei	Adipose
36	chr3:98496600-98503800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:98496800-98498600	Enhancers	Right Atrium	heart
38	chr3:98496800-98499200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:98496800-98499200	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr3:98496800-98502800	Weak transcription	Fetal Thymus	thymus
41	chr3:98497000-98498400	Enhancers	GM12878-XiMat	blood
42	chr3:98497000-98524600	Weak transcription	Fetal Brain Male	brain
43	chr3:98497200-98498400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr3:98497200-98499200	Enhancers	Fetal Kidney	kidney
45	chr3:98497400-98498400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr3:98497400-98498600	Enhancers	Left Ventricle	heart
47	chr3:98497400-98498600	Enhancers	Right Ventricle	heart
48	chr3:98497400-98498600	Flanking Active TSS	Osteobl	bone
49	chr3:98497400-98499600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr3:98497400-98499800	Strong transcription	Dnd41	blood

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