Variant report

Variant	rs16834090
Chromosome Location	chr1:152432904-152432905
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:152427149..152431116-chr1:152432687..152434302,3	MCF-7	breast:
2	chr1:152432539..152433414-chr6:8612704..8613456,2	MCF-7	breast:
3	chr1:152199924..152200497-chr1:152432483..152433028,2	MCF-7	breast:
4	chr1:152431515..152433296-chr20:52368931..52371205,2	MCF-7	breast:
5	chr1:152006513..152009632-chr1:152432632..152435918,6	MCF-7	breast:
6	chr1:152379125..152381578-chr1:152431090..152434005,2	MCF-7	breast:
7	chr1:152432248..152432959-chr20:52560044..52560553,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163191	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10888488	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11205002	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11205003	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11205004	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11205008	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11578573	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11579024	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11579085	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11803629	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12069640	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12125681	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12749879	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1885527	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1885528	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1885529	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1923491	0.87[CEU][hapmap]
rs1923498	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1923499	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2146117	0.80[GIH][hapmap]
rs4240878	0.80[AFR][1000 genomes]
rs4557976	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4636462	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845433	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4845435	0.93[ASN][1000 genomes]
rs4845436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845438	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845440	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4845766	0.88[CEU][hapmap]
rs4845767	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4845768	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4845769	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4845770	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4845771	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845775	0.94[ASN][1000 genomes]
rs4991216	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs499997	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs556124	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6587674	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6695950	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6696556	0.81[GIH][hapmap]
rs7529997	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7548609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs986903	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014095	chr1:152104486-152454591	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1005472	chr1:152247763-152443448	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv535161	chr1:152247763-152443448	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv916016	chr1:152337775-152590520	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv872443	chr1:152400055-152459747	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv872444	chr1:152400361-152440753	ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv824664	chr1:152409024-152434443	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv463850	chr1:152411090-152434009	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv547858	chr1:152411090-152434009	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv872445	chr1:152411813-152440753	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16834090	SLC27A3	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152432200-152433000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
2	chr1:152432200-152433000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:152432200-152433000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:152432200-152433000	Active TSS	HepG2	liver
5	chr1:152432200-152433000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr1:152432200-152433000	Enhancers	NHDF-Ad	bronchial
7	chr1:152432200-152433200	Enhancers	Primary hematopoietic stem cells	blood
8	chr1:152432200-152433200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:152432200-152433600	Flanking Active TSS	GM12878-XiMat	blood
10	chr1:152432400-152433000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:152432400-152433000	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr1:152432400-152433000	Enhancers	Primary B cells from cord blood	blood
13	chr1:152432400-152433000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
14	chr1:152432400-152433000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
15	chr1:152432400-152433000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
16	chr1:152432400-152433000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
17	chr1:152432400-152433000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
18	chr1:152432400-152433000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:152432400-152433000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:152432400-152433000	Enhancers	Colon Smooth Muscle	Colon
21	chr1:152432400-152433000	Flanking Active TSS	Duodenum Mucosa	Duodenum
22	chr1:152432400-152433000	Enhancers	Fetal Lung	lung
23	chr1:152432400-152433000	Enhancers	Placenta	Placenta
24	chr1:152432400-152433000	Enhancers	Fetal Thymus	thymus
25	chr1:152432400-152433000	Active TSS	Rectal Smooth Muscle	rectum
26	chr1:152432400-152433000	Enhancers	Spleen	Spleen
27	chr1:152432400-152433000	Active TSS	HSMM	muscle
28	chr1:152432400-152433000	Enhancers	NHEK	skin
29	chr1:152432400-152433200	Enhancers	Primary T cells from cord blood	blood
30	chr1:152432400-152433200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
31	chr1:152432400-152433200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:152432400-152433200	Enhancers	Aorta	Aorta
33	chr1:152432400-152433400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr1:152432400-152433400	Enhancers	HMEC	breast
35	chr1:152432600-152433000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
36	chr1:152432600-152433000	Active TSS	Brain Anterior Caudate	brain
37	chr1:152432600-152433000	Enhancers	Stomach Mucosa	stomach
38	chr1:152432600-152433200	Enhancers	Dnd41	blood
39	chr1:152432800-152433000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:152432800-152433000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:152432800-152433000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
42	chr1:152432800-152433000	Flanking Active TSS	Primary B cells from peripheral blood	blood
43	chr1:152432800-152433000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
44	chr1:152432800-152433000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr1:152432800-152433000	Active TSS	Adipose Nuclei	Adipose
46	chr1:152432800-152433000	Active TSS	Liver	Liver
47	chr1:152432800-152433000	Enhancers	Right Atrium	heart
48	chr1:152432800-152433000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr1:152432800-152433000	Enhancers	Thymus	Thymus
50	chr1:152432800-152433000	Flanking Active TSS	NHLF	lung

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