Variant report

Variant	rs28866814
Chromosome Location	chr3:112308839-112308840
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:112308556..112310360-chr3:112358622..112360882,2	MCF-7	breast:
2	chr3:112304467..112306761-chr3:112307873..112309830,2	K562	blood:

Variant related genes	Relation type
ENSG00000091986	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10755071	0.84[ASN][1000 genomes]
rs11489073	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11706550	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1512005	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1512006	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1844089	0.89[EUR][1000 genomes]
rs1877363	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1994713	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2101632	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2131008	0.82[EUR][1000 genomes]
rs2172196	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2279532	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2280066	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464611	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2633555	0.84[EUR][1000 genomes]
rs2633578	0.87[EUR][1000 genomes]
rs2633580	0.87[EUR][1000 genomes]
rs2633582	0.89[EUR][1000 genomes]
rs2633584	0.86[EUR][1000 genomes]
rs2638016	0.82[EUR][1000 genomes]
rs2638022	0.82[EUR][1000 genomes]
rs2638031	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2638042	0.82[EUR][1000 genomes]
rs2668217	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2668220	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2668222	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2668223	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2705517	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2705531	0.89[EUR][1000 genomes]
rs2705532	0.83[EUR][1000 genomes]
rs2705534	0.89[EUR][1000 genomes]
rs2705543	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2705566	0.87[EUR][1000 genomes]
rs2933142	0.81[ASN][1000 genomes]
rs2952323	0.91[EUR][1000 genomes]
rs34233684	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3732815	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682413	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5000995	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6772077	0.81[ASN][1000 genomes]
rs6774355	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6792947	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7625366	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7652377	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs766968	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9288954	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9756562	0.89[EUR][1000 genomes]
rs9809247	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9848054	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9854043	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9866734	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9869455	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9869579	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877342	chr3:112185025-112332629	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	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
3	nsv591301	chr3:112252532-112332629	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28866814	SLC35A5	cis	Nerve Tibial	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112281800-112312000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:112281800-112315400	Weak transcription	Pancreas	Pancrea
3	chr3:112281800-112324200	Weak transcription	Spleen	Spleen
4	chr3:112281800-112325400	Weak transcription	Gastric	stomach
5	chr3:112282000-112312200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:112282000-112330400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:112282000-112330600	Weak transcription	Esophagus	oesophagus
8	chr3:112282400-112312400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr3:112282400-112316800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:112282400-112322800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:112282400-112324200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:112282400-112340000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr3:112283000-112316400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr3:112290400-112317400	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr3:112290600-112315600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:112291600-112320600	Weak transcription	NHLF	lung
17	chr3:112293200-112315600	Weak transcription	NH-A	brain
18	chr3:112293200-112318000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr3:112295400-112311200	Weak transcription	Fetal Intestine Small	intestine
20	chr3:112296600-112309800	Strong transcription	Placenta	Placenta
21	chr3:112297800-112309800	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr3:112298600-112325200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:112298800-112335200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:112299200-112311000	Weak transcription	HUVEC	blood vessel
25	chr3:112299200-112311000	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr3:112299200-112315000	Weak transcription	NHEK	skin
27	chr3:112299400-112309400	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr3:112300200-112315800	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr3:112300200-112317400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:112300200-112331000	Weak transcription	Lung	lung
31	chr3:112300200-112334000	Weak transcription	Fetal Stomach	stomach
32	chr3:112301200-112311200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr3:112301600-112315600	Weak transcription	Stomach Mucosa	stomach
34	chr3:112301600-112316600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr3:112301800-112311600	Weak transcription	A549	lung
36	chr3:112302000-112309600	Strong transcription	Adipose Nuclei	Adipose
37	chr3:112302000-112313800	Weak transcription	Dnd41	blood
38	chr3:112302000-112317400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr3:112302600-112322800	Weak transcription	Colon Smooth Muscle	Colon
40	chr3:112302800-112324200	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr3:112303400-112317000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr3:112303600-112322800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr3:112303800-112311000	Weak transcription	GM12878-XiMat	blood
44	chr3:112303800-112312200	Weak transcription	Brain Angular Gyrus	brain
45	chr3:112303800-112324200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr3:112304000-112311400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr3:112304000-112320400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr3:112304200-112311400	Weak transcription	Psoas Muscle	Psoas
49	chr3:112304200-112317600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr3:112304400-112312000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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