Variant report

Variant	rs28535523
Chromosome Location	chr3:49848414-49848415
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49823748..49825794-chr3:49847684..49850638,2	MCF-7	breast:
2	chr3:49842643..49844250-chr3:49847224..49849823,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176095	Chromatin interaction
ENSG00000263506	Chromatin interaction
ENSG00000182179	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11130217	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11709734	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11720705	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12715437	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1491985	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1799844	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1996663	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1996664	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3020779	0.81[EUR][1000 genomes]
rs35129566	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55997059	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58339610	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59357103	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59684465	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61557789	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62260663	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62260720	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62260723	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62262722	0.95[EUR][1000 genomes]
rs62262730	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6790568	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6804970	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6809879	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7613603	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7620848	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7621797	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7628207	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7637711	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7649428	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9829155	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9835157	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9836756	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9851651	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9870755	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9870858	0.91[AMR][1000 genomes];0.94[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	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv834688	chr3:49811115-50019299	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv1809827	chr3:49812331-49934179	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv876766	chr3:49817450-49961780	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv967270	chr3:49845381-49870409	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs28535523	NICN1	cis	Thyroid	GTEx
rs28535523	AMT	cis	Thyroid	GTEx
rs28535523	AMT	cis	lung	GTEx

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49841600-49850400	Weak transcription	Small Intestine	intestine
2	chr3:49842000-49850600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:49843400-49866400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:49843600-49850400	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr3:49843600-49850600	Weak transcription	HSMM	muscle
6	chr3:49843600-49850800	Weak transcription	Psoas Muscle	Psoas
7	chr3:49844000-49850200	Weak transcription	NHDF-Ad	bronchial
8	chr3:49844400-49850200	Genic enhancers	Spleen	Spleen
9	chr3:49844800-49849400	Strong transcription	Duodenum Mucosa	Duodenum
10	chr3:49845000-49849600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr3:49845000-49850600	Genic enhancers	Primary B cells from peripheral blood	blood
12	chr3:49845000-49850600	Weak transcription	NH-A	brain
13	chr3:49845200-49848600	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr3:49845200-49850000	Strong transcription	Colonic Mucosa	Colon
15	chr3:49845400-49849600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr3:49845400-49849800	Weak transcription	Brain Substantia Nigra	brain
17	chr3:49845400-49850000	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr3:49845400-49850000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:49845400-49850000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr3:49845400-49850000	Weak transcription	Brain Cingulate Gyrus	brain
21	chr3:49845400-49850000	Weak transcription	Stomach Mucosa	stomach
22	chr3:49845400-49850600	Weak transcription	HepG2	liver
23	chr3:49845600-49849000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:49845600-49849200	Strong transcription	Stomach Smooth Muscle	stomach
25	chr3:49845600-49849600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr3:49845600-49850000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:49845600-49850000	Weak transcription	HMEC	breast
28	chr3:49845600-49850600	Weak transcription	HUVEC	blood vessel
29	chr3:49845600-49850800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:49845800-49848600	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr3:49845800-49849000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr3:49845800-49849400	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr3:49845800-49849800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr3:49845800-49849800	Weak transcription	Right Atrium	heart
35	chr3:49845800-49850400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr3:49845800-49850400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr3:49845800-49850800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:49846000-49848600	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr3:49846000-49849000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr3:49846000-49849000	Strong transcription	Adipose Nuclei	Adipose
41	chr3:49846000-49849000	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr3:49846000-49849600	Strong transcription	GM12878-XiMat	blood
43	chr3:49846000-49849800	Strong transcription	Fetal Intestine Small	intestine
44	chr3:49846000-49849800	Strong transcription	Gastric	stomach
45	chr3:49846000-49850600	Weak transcription	NHEK	skin
46	chr3:49846200-49848600	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr3:49846200-49849400	Strong transcription	Pancreas	Pancrea
48	chr3:49846200-49849600	Strong transcription	Colon Smooth Muscle	Colon
49	chr3:49846200-49849800	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr3:49846200-49850000	Weak transcription	Brain Hippocampus Middle	brain

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