Variant report

Variant	rs16903338
Chromosome Location	chr5:14253187-14253188
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:14141623..14144642-chr5:14252312..14255113,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000038382	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs12659261	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs154150	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs154153	0.81[EUR][1000 genomes]
rs154154	0.81[EUR][1000 genomes]
rs154155	0.81[EUR][1000 genomes]
rs164859	0.90[JPT][hapmap]
rs164860	0.90[JPT][hapmap]
rs164862	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs164863	0.81[JPT][hapmap]
rs165083	0.81[EUR][1000 genomes]
rs165092	0.82[JPT][hapmap]
rs165094	0.86[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs165095	0.82[JPT][hapmap]
rs165096	0.84[ASN][1000 genomes]
rs16903326	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2440982	0.90[JPT][hapmap]
rs247142	0.85[CEU][hapmap]
rs30603	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs30604	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs30605	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs30618	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs30621	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs30628	0.90[JPT][hapmap]
rs354303	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs39857	0.85[CEU][hapmap]
rs42204	0.85[EUR][1000 genomes]
rs42405	0.81[EUR][1000 genomes]
rs42551	0.85[CEU][hapmap];0.83[TSI][hapmap]
rs56226439	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56334634	0.87[ASN][1000 genomes]
rs58221971	0.85[ASN][1000 genomes]
rs6554849	0.85[ASN][1000 genomes]
rs6554850	0.87[ASN][1000 genomes]
rs6554851	0.87[ASN][1000 genomes]
rs67084079	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72744279	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7380307	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7700787	0.95[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1825924	chr5:14147376-14270450	Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv830209	chr5:14154989-14301758	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv948355	chr5:14160447-14395478	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1026914	chr5:14237782-14751588	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16903338	LOC285696	cis	parietal	SCAN
rs16903338	FAM105B	cis	cerebellum	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14247200-14256800	Weak transcription	Stomach Mucosa	stomach
2	chr5:14247400-14254600	Weak transcription	Hela-S3	cervix
3	chr5:14247400-14257000	Weak transcription	Gastric	stomach
4	chr5:14248400-14253800	Enhancers	Fetal Muscle Trunk	muscle
5	chr5:14248400-14255400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr5:14248600-14255000	Enhancers	Psoas Muscle	Psoas
7	chr5:14248800-14253800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr5:14248800-14254000	Enhancers	Fetal Thymus	thymus
9	chr5:14249400-14253200	Enhancers	H1 Cell Line	embryonic stem cell
10	chr5:14249400-14253200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:14249400-14253200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr5:14249400-14254800	Enhancers	Lung	lung
13	chr5:14249600-14256400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr5:14250000-14254000	Enhancers	Thymus	Thymus
15	chr5:14250600-14255200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr5:14250800-14253200	Enhancers	Adipose Nuclei	Adipose
17	chr5:14250800-14253200	Enhancers	Brain Anterior Caudate	brain
18	chr5:14250800-14253800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr5:14250800-14253800	Weak transcription	K562	blood
20	chr5:14250800-14255200	Weak transcription	NHDF-Ad	bronchial
21	chr5:14250800-14256200	Weak transcription	Small Intestine	intestine
22	chr5:14250800-14256400	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr5:14250800-14256800	Weak transcription	Ovary	ovary
24	chr5:14250800-14257000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr5:14251200-14253200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr5:14251200-14256200	Weak transcription	HepG2	liver
27	chr5:14251400-14253800	Weak transcription	HUVEC	blood vessel
28	chr5:14251400-14254200	Weak transcription	Fetal Intestine Small	intestine
29	chr5:14251400-14255000	Enhancers	Left Ventricle	heart
30	chr5:14251400-14255200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr5:14251400-14257200	Weak transcription	Duodenum Mucosa	Duodenum
32	chr5:14251600-14255200	Weak transcription	Osteobl	bone
33	chr5:14251800-14253800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr5:14251800-14254600	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr5:14251800-14254600	Weak transcription	Spleen	Spleen
36	chr5:14251800-14254600	Weak transcription	HSMMtube	muscle
37	chr5:14251800-14254600	Weak transcription	NH-A	brain
38	chr5:14251800-14255200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr5:14251800-14256400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr5:14251800-14257200	Weak transcription	Brain Angular Gyrus	brain
41	chr5:14252000-14253200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr5:14252000-14255200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr5:14252000-14255200	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr5:14252000-14256000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr5:14252000-14256400	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr5:14252000-14256400	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr5:14252000-14256800	Weak transcription	Fetal Stomach	stomach
48	chr5:14252000-14258200	Weak transcription	Brain Hippocampus Middle	brain
49	chr5:14252200-14253200	Enhancers	Aorta	Aorta
50	chr5:14252200-14254200	Enhancers	Fetal Heart	heart

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