Variant report

Variant	rs13084692
Chromosome Location	chr3:98609449-98609450
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:98603937..98606892-chr3:98607336..98610177,2	MCF-7	breast:
2	chr3:98607825..98610061-chr3:98619024..98621241,2	K562	blood:
3	chr3:98606929..98610886-chr3:98613079..98616999,4	K562	blood:

Variant related genes	Relation type
ENSG00000057019	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10428160	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10589669	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11552978	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12107272	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12108018	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12108142	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13059624	0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs13065136	0.98[EUR][1000 genomes]
rs13068317	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13072410	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13074614	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13074787	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13076960	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13078549	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs13079960	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13080057	0.87[EUR][1000 genomes]
rs13081992	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13083238	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13083613	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13083934	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13087627	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13087631	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13088532	0.89[EUR][1000 genomes]
rs13091170	0.98[EUR][1000 genomes]
rs13091236	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13091956	0.82[EUR][1000 genomes]
rs13093128	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13096085	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13097876	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13100915	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13100937	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1983009	0.84[EUR][1000 genomes]
rs2439232	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[EUR][1000 genomes]
rs2454687	0.89[EUR][1000 genomes]
rs34008360	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34269725	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34279227	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34284740	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34394867	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34428696	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34458031	0.91[AMR][1000 genomes]
rs34470469	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34479374	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34489202	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34688367	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34711372	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34725039	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34791359	0.91[AMR][1000 genomes]
rs34826460	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34848749	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34860591	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35006699	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35025156	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35076733	0.93[EUR][1000 genomes]
rs35098355	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35103318	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35219252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35234681	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35239055	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35312318	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35366262	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35422064	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35499232	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35514544	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35526367	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35539438	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35592768	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35764973	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35854439	0.82[EUR][1000 genomes]
rs35894621	0.91[AMR][1000 genomes]
rs35914268	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35947493	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35947806	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36028944	0.82[AMR][1000 genomes]
rs36032715	0.87[EUR][1000 genomes]
rs36098932	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36157152	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36160001	0.84[EUR][1000 genomes]
rs36175276	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs41267851	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55644421	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56083233	0.98[EUR][1000 genomes]
rs56094988	0.82[EUR][1000 genomes]
rs56246599	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56408882	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6764579	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6805362	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71124004	0.83[EUR][1000 genomes]
rs71311393	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71311394	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71311397	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71311398	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71311402	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71313504	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71313506	0.91[EUR][1000 genomes]
rs71313508	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71313509	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71313510	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71313511	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71313512	0.91[AMR][1000 genomes]
rs7614053	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[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
rs13084692	ST3GAL6	cis	lymphoblastoid	seeQTL

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98583400-98611400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:98590000-98609600	Weak transcription	Brain Anterior Caudate	brain
3	chr3:98593800-98619400	Weak transcription	Small Intestine	intestine
4	chr3:98594400-98616600	Weak transcription	Fetal Brain Male	brain
5	chr3:98597400-98619000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr3:98599800-98618400	Weak transcription	Fetal Brain Female	brain
7	chr3:98600000-98609600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr3:98600600-98611200	Weak transcription	Liver	Liver
9	chr3:98600600-98613000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:98600600-98618000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr3:98600600-98618000	Weak transcription	Fetal Thymus	thymus
12	chr3:98602200-98613600	Genic enhancers	HSMM	muscle
13	chr3:98602400-98613600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:98603200-98612600	Genic enhancers	NHEK	skin
15	chr3:98604000-98613000	Enhancers	NHLF	lung
16	chr3:98604200-98612600	Enhancers	NHDF-Ad	bronchial
17	chr3:98604400-98610400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:98604400-98611400	Genic enhancers	HMEC	breast
19	chr3:98604400-98614600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:98604800-98609600	Genic enhancers	Osteobl	bone
21	chr3:98604800-98609800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:98604800-98612600	Weak transcription	Fetal Muscle Leg	muscle
23	chr3:98605000-98610400	Weak transcription	Left Ventricle	heart
24	chr3:98605000-98610400	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr3:98605000-98618600	Weak transcription	Fetal Stomach	stomach
26	chr3:98605400-98609600	Weak transcription	Aorta	Aorta
27	chr3:98605400-98609800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr3:98605400-98610600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr3:98605400-98611400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:98605600-98609800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr3:98606000-98610000	Transcr. at gene 5' and 3'	A549	lung
32	chr3:98606200-98609600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:98606200-98609800	Weak transcription	Colon Smooth Muscle	Colon
34	chr3:98606200-98610000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:98606200-98610400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:98606400-98618400	Weak transcription	Fetal Kidney	kidney
37	chr3:98606600-98611200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:98606600-98612600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr3:98606600-98618000	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr3:98606800-98610000	Transcr. at gene 5' and 3'	NH-A	brain
41	chr3:98607000-98610400	Genic enhancers	Muscle Satellite Cultured Cells	--
42	chr3:98607600-98611800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:98607800-98612000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:98608000-98609800	Weak transcription	HSMMtube	muscle
45	chr3:98608000-98611200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr3:98608000-98612400	Weak transcription	Brain Hippocampus Middle	brain
47	chr3:98608400-98611000	Weak transcription	HepG2	liver
48	chr3:98608600-98609800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr3:98608600-98610800	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr3:98608800-98610000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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