Variant report

Variant	rs9855175
Chromosome Location	chr3:98500100-98500101
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs1062196	0.96[ASN][1000 genomes]
rs12107050	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12330170	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12490832	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13060012	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs14310	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1440150	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1440151	0.81[AMR][1000 genomes]
rs17270593	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1866677	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1866678	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1866679	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2028393	0.81[EUR][1000 genomes]
rs2119188	0.81[EUR][1000 genomes]
rs2262597	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2290067	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2334230	0.81[AMR][1000 genomes]
rs2439213	0.87[EUR][1000 genomes]
rs2439215	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2439218	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2439225	0.80[EUR][1000 genomes]
rs2439228	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2439229	0.85[ASN][1000 genomes]
rs2439231	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2439236	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2454677	0.81[ASN][1000 genomes]
rs2454685	0.83[EUR][1000 genomes]
rs2470859	0.81[EUR][1000 genomes]
rs2470867	0.85[ASN][1000 genomes]
rs2470869	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2470879	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2470881	0.81[EUR][1000 genomes]
rs28802000	0.91[ASN][1000 genomes]
rs2919234	0.85[ASN][1000 genomes]
rs2919236	0.85[ASN][1000 genomes]
rs34234373	0.91[ASN][1000 genomes]
rs34558202	0.91[ASN][1000 genomes]
rs3755574	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3755576	0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3772098	0.81[AMR][1000 genomes]
rs3772101	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3772102	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3821359	0.81[AMR][1000 genomes]
rs4425200	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4425201	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4426625	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4426626	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4494869	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs62278486	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6782630	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6785935	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6788418	0.91[ASN][1000 genomes]
rs6788689	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6790650	0.91[ASN][1000 genomes]
rs6804850	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6808116	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs704585	1.00[ASN][1000 genomes]
rs7431448	0.81[AMR][1000 genomes]
rs7611929	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7612036	0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7616275	0.91[ASN][1000 genomes]
rs828609	0.98[ASN][1000 genomes]
rs844160	0.80[AMR][1000 genomes]
rs9811305	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9811449	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9811860	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9814819	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9815226	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9823430	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9845558	0.91[ASN][1000 genomes]
rs9860216	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9866570	0.81[AMR][1000 genomes]
rs9867586	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9872152	0.81[AMR][1000 genomes]
rs9873932	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9878392	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9881519	0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9883516	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9883537	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs999147	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[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
rs9855175	ST3GAL6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:76 , 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	chr3:98494600-98506000	Enhancers	Aorta	Aorta
14	chr3:98496600-98503800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:98496800-98502800	Weak transcription	Fetal Thymus	thymus
16	chr3:98497000-98524600	Weak transcription	Fetal Brain Male	brain
17	chr3:98497400-98501800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:98497400-98503600	Enhancers	Placenta	Placenta
19	chr3:98497600-98502400	Weak transcription	Lung	lung
20	chr3:98497800-98517200	Weak transcription	Fetal Brain Female	brain
21	chr3:98498000-98500400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:98498000-98500400	Weak transcription	Pancreas	Pancrea
23	chr3:98498000-98501800	Weak transcription	Gastric	stomach
24	chr3:98498000-98503000	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr3:98498000-98516600	Weak transcription	Stomach Mucosa	stomach
26	chr3:98498200-98505400	Strong transcription	Thymus	Thymus
27	chr3:98498400-98501600	Weak transcription	GM12878-XiMat	blood
28	chr3:98498400-98504600	Weak transcription	Fetal Intestine Small	intestine
29	chr3:98498600-98503000	Weak transcription	Right Atrium	heart
30	chr3:98498800-98500600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr3:98498800-98502000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:98498800-98506800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr3:98498800-98512800	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr3:98499000-98503000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:98499000-98503000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr3:98499000-98504200	Weak transcription	HSMM	muscle
37	chr3:98499200-98500400	Weak transcription	Right Ventricle	heart
38	chr3:98499200-98500800	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr3:98499200-98501200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr3:98499200-98501200	Weak transcription	Fetal Kidney	kidney
41	chr3:98499200-98501800	Weak transcription	NHEK	skin
42	chr3:98499200-98502200	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr3:98499200-98503200	Weak transcription	NHDF-Ad	bronchial
44	chr3:98499200-98503400	Weak transcription	NHLF	lung
45	chr3:98499200-98504200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr3:98499200-98504600	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr3:98499200-98516600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr3:98499400-98503000	Weak transcription	Fetal Heart	heart
49	chr3:98499400-98503600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:98499400-98506400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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