Variant report

Variant	rs2439225
Chromosome Location	chr3:98609291-98609292
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: 120 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs1123293	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12054181	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1383905	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs14310	0.83[EUR][1000 genomes]
rs1440150	0.81[ASN][1000 genomes]
rs1481634	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1481635	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1481636	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1481637	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1837500	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1866677	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1866678	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1866679	0.84[EUR][1000 genomes]
rs1875086	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1967009	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2028393	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2119187	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2119188	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2128051	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2128054	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2246861	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2249740	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2262597	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2290067	0.83[EUR][1000 genomes]
rs2439213	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2439214	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2439215	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2439217	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2439218	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[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];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439223	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2439224	0.81[ASN][1000 genomes]
rs2439226	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2439228	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2439229	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2439231	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2439236	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2449001	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2449039	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2449040	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2449041	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2449042	0.81[AMR][1000 genomes];0.84[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	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[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];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2454686	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2454691	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2470821	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2470822	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2470823	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2470824	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2470825	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2470826	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2470845	0.82[ASN][1000 genomes]
rs2470851	0.86[ASN][1000 genomes]
rs2470857	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2470859	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[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];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2470876	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2470879	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2470881	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[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	0.80[EUR][1000 genomes]
rs2960190	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34234373	0.81[ASN][1000 genomes]
rs34558202	0.81[ASN][1000 genomes]
rs3755574	0.81[EUR][1000 genomes]
rs4425200	0.83[EUR][1000 genomes]
rs4426625	0.83[EUR][1000 genomes]
rs4450736	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62276887	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6440280	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6782630	0.83[EUR][1000 genomes]
rs6785935	0.81[ASN][1000 genomes]
rs6788418	0.81[ASN][1000 genomes]
rs6788689	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6804850	0.83[EUR][1000 genomes]
rs7616275	0.81[ASN][1000 genomes]
rs7630800	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7631624	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	0.82[EUR][1000 genomes]
rs9811860	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9814819	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9815226	0.83[EUR][1000 genomes]
rs9820384	0.81[ASN][1000 genomes]
rs9823430	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9835142	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9843864	0.81[AMR][1000 genomes];0.84[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];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9855175	0.80[EUR][1000 genomes]
rs9860216	0.81[ASN][1000 genomes]
rs9860264	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9867586	0.85[EUR][1000 genomes]
rs9873932	0.81[ASN][1000 genomes]
rs9883516	0.84[EUR][1000 genomes]
rs9883537	0.84[EUR][1000 genomes]
rs999147	0.83[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
rs2439225	ST3GAL6	Cis_1M	lymphoblastoid	RTeQTL

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	chr3:98599200-98609400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:98599800-98618400	Weak transcription	Fetal Brain Female	brain
8	chr3:98600000-98609600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:98600600-98611200	Weak transcription	Liver	Liver
10	chr3:98600600-98613000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:98600600-98618000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr3:98600600-98618000	Weak transcription	Fetal Thymus	thymus
13	chr3:98602200-98613600	Genic enhancers	HSMM	muscle
14	chr3:98602400-98613600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:98603200-98612600	Genic enhancers	NHEK	skin
16	chr3:98604000-98613000	Enhancers	NHLF	lung
17	chr3:98604200-98612600	Enhancers	NHDF-Ad	bronchial
18	chr3:98604400-98610400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr3:98604400-98611400	Genic enhancers	HMEC	breast
20	chr3:98604400-98614600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:98604800-98609400	Weak transcription	Right Atrium	heart
22	chr3:98604800-98609600	Genic enhancers	Osteobl	bone
23	chr3:98604800-98609800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:98604800-98612600	Weak transcription	Fetal Muscle Leg	muscle
25	chr3:98605000-98610400	Weak transcription	Left Ventricle	heart
26	chr3:98605000-98610400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr3:98605000-98618600	Weak transcription	Fetal Stomach	stomach
28	chr3:98605400-98609400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr3:98605400-98609600	Weak transcription	Aorta	Aorta
30	chr3:98605400-98609800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr3:98605400-98610600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr3:98605400-98611400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:98605600-98609400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:98605600-98609800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr3:98606000-98610000	Transcr. at gene 5' and 3'	A549	lung
36	chr3:98606200-98609600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr3:98606200-98609800	Weak transcription	Colon Smooth Muscle	Colon
38	chr3:98606200-98610000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:98606200-98610400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:98606400-98618400	Weak transcription	Fetal Kidney	kidney
41	chr3:98606600-98611200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr3:98606600-98612600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr3:98606600-98618000	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:98606800-98610000	Transcr. at gene 5' and 3'	NH-A	brain
45	chr3:98607000-98610400	Genic enhancers	Muscle Satellite Cultured Cells	--
46	chr3:98607600-98611800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr3:98607800-98612000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:98608000-98609400	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr3:98608000-98609800	Weak transcription	HSMMtube	muscle
50	chr3:98608000-98611200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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