Variant report

Variant	rs1398091
Chromosome Location	chr3:112332809-112332810
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1105938	0.85[AMR][1000 genomes]
rs12632867	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs1386895	1.00[CEU][hapmap];0.81[GIH][hapmap];0.80[EUR][1000 genomes]
rs1512006	0.82[CEU][hapmap];0.91[GIH][hapmap]
rs1533159	0.84[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs1814052	0.89[EUR][1000 genomes]
rs1873571	0.85[GIH][hapmap]
rs1873572	0.92[JPT][hapmap]
rs1877363	0.82[CEU][hapmap];0.91[GIH][hapmap]
rs2137199	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2171513	0.82[CEU][hapmap];0.86[JPT][hapmap]
rs2171514	0.86[EUR][1000 genomes]
rs2292442	0.82[AMR][1000 genomes]
rs2633557	0.83[EUR][1000 genomes]
rs2633560	0.83[EUR][1000 genomes]
rs2633562	1.00[CEU][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes]
rs2633563	0.86[EUR][1000 genomes]
rs2633574	0.81[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs2633578	0.82[CEU][hapmap];0.81[GIH][hapmap]
rs2633579	1.00[CEU][hapmap];0.92[JPT][hapmap];0.89[EUR][1000 genomes]
rs2633580	0.82[CEU][hapmap];0.81[GIH][hapmap]
rs2633588	0.89[EUR][1000 genomes]
rs2633589	0.89[EUR][1000 genomes]
rs2638013	0.89[EUR][1000 genomes]
rs2638015	0.86[EUR][1000 genomes]
rs2638019	0.92[JPT][hapmap]
rs2638022	0.85[GIH][hapmap]
rs2638023	0.81[CHD][hapmap];0.92[JPT][hapmap]
rs2638026	0.81[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs2638029	0.92[JPT][hapmap]
rs2638031	0.85[GIH][hapmap]
rs2638032	0.92[JPT][hapmap]
rs2638035	0.84[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.88[TSI][hapmap]
rs2638037	0.85[GIH][hapmap]
rs2638039	0.92[JPT][hapmap]
rs2668219	0.85[AMR][1000 genomes]
rs2705507	0.81[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs2705515	0.85[AMR][1000 genomes]
rs2705518	0.85[AMR][1000 genomes]
rs2705521	0.81[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs2705522	0.92[JPT][hapmap]
rs2705525	0.89[EUR][1000 genomes]
rs2705533	0.89[EUR][1000 genomes]
rs2705534	0.82[CEU][hapmap];0.81[GIH][hapmap]
rs2705535	0.92[JPT][hapmap]
rs2705536	0.89[EUR][1000 genomes]
rs2705541	0.92[JPT][hapmap];0.85[AMR][1000 genomes]
rs2705544	1.00[CEU][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs2705555	0.83[EUR][1000 genomes]
rs2705556	0.92[JPT][hapmap]
rs2705562	0.92[JPT][hapmap]
rs2705565	1.00[CEU][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs2933134	0.81[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs2933135	0.84[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs2933137	0.82[AMR][1000 genomes]
rs2952319	0.84[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap]
rs2952320	0.85[AMR][1000 genomes]
rs2952323	0.82[CEU][hapmap]
rs2952325	0.90[JPT][hapmap]
rs2969895	0.89[JPT][hapmap]
rs2969896	0.81[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];1.00[TSI][hapmap]
rs2971204	1.00[CEU][hapmap];0.92[JPT][hapmap];0.89[EUR][1000 genomes]
rs4682410	0.82[CEU][hapmap];0.81[GIH][hapmap];0.80[EUR][1000 genomes]
rs6438079	1.00[CEU][hapmap];0.81[GIH][hapmap];0.80[EUR][1000 genomes]
rs6792947	0.82[CEU][hapmap];0.91[GIH][hapmap]
rs728568	0.92[JPT][hapmap];0.82[AMR][1000 genomes]
rs751875	0.85[AMR][1000 genomes]
rs7652377	0.82[CEU][hapmap]
rs766968	0.82[CEU][hapmap];0.91[GIH][hapmap]
rs9288952	0.82[CEU][hapmap]
rs9848054	0.82[CEU][hapmap]
rs9866734	0.82[CEU][hapmap]
rs9869455	1.00[CEU][hapmap]
rs9869579	1.00[CEU][hapmap]
rs998036	0.84[CHD][hapmap];0.89[GIH][hapmap];0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1398091	SLC35A5	cis	lymphoblastoid	seeQTL

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112282400-112340000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr3:112298800-112335200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:112300200-112334000	Weak transcription	Fetal Stomach	stomach
4	chr3:112305800-112334800	Weak transcription	Aorta	Aorta
5	chr3:112312600-112346200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr3:112312600-112347200	Weak transcription	Fetal Intestine Large	intestine
7	chr3:112316200-112342800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr3:112316400-112333600	Weak transcription	A549	lung
9	chr3:112316600-112337600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr3:112318000-112341800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:112322200-112337200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:112323800-112334600	Weak transcription	Fetal Muscle Leg	muscle
13	chr3:112326000-112333400	Weak transcription	Ovary	ovary
14	chr3:112327800-112340600	Weak transcription	Fetal Kidney	kidney
15	chr3:112329000-112334400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr3:112329200-112333400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr3:112329400-112333400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:112329400-112333400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:112329400-112334200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr3:112329600-112341800	Strong transcription	HSMM	muscle
21	chr3:112330000-112335000	Strong transcription	Muscle Satellite Cultured Cells	--
22	chr3:112330000-112336600	Strong transcription	NHDF-Ad	bronchial
23	chr3:112330200-112338400	Strong transcription	HSMMtube	muscle
24	chr3:112330400-112335000	Strong transcription	NH-A	brain
25	chr3:112330400-112346800	Strong transcription	NHLF	lung
26	chr3:112330600-112333600	Weak transcription	Colon Smooth Muscle	Colon
27	chr3:112331200-112334000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:112331200-112334400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:112331200-112334800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr3:112331200-112335400	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr3:112331200-112351600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:112331400-112333400	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr3:112331400-112333400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:112331400-112333400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:112331400-112334200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr3:112331400-112354800	Weak transcription	Psoas Muscle	Psoas
37	chr3:112331600-112334200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr3:112331600-112334600	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr3:112331600-112335800	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr3:112331600-112337400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:112331600-112337800	Weak transcription	HUVEC	blood vessel
42	chr3:112331600-112338200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr3:112331600-112338400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:112331800-112333400	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr3:112331800-112334800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr3:112331800-112336200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:112332000-112333400	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr3:112332200-112335000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:112332200-112337800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:112332400-112335200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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