Variant report

Variant	rs4497676
Chromosome Location	chr16:69814950-69814951
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:69787238..69789722-chr16:69814157..69817043,3	MCF-7	breast:
2	chr16:69796024..69797928-chr16:69813694..69816439,2	MCF-7	breast:
3	chr16:69807100..69810099-chr16:69813476..69816910,4	K562	blood:

Variant related genes	Relation type
ENSG00000198373	Chromatin interaction
ENSG00000141101	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10454066	1.00[CEU][hapmap]
rs10500551	1.00[CEU][hapmap]
rs10852458	1.00[CEU][hapmap]
rs11075733	0.86[EUR][1000 genomes]
rs11075734	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1139178	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11639947	1.00[CEU][hapmap]
rs11641233	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs11641521	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11643926	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11644838	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11644914	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12232410	0.95[CEU][hapmap]
rs12446201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12595869	1.00[CEU][hapmap]
rs12596679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12596823	0.95[CEU][hapmap]
rs12925371	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1437135	1.00[CEU][hapmap]
rs16958970	1.00[CEU][hapmap]
rs16959025	1.00[CEU][hapmap]
rs1800566	1.00[CEU][hapmap]
rs2361838	1.00[CEU][hapmap]
rs3169315	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs3743673	1.00[CEU][hapmap]
rs3811349	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4078387	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4464069	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4580150	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985518	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4985523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55701476	0.81[EUR][1000 genomes]
rs55863174	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55992518	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56282083	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57518557	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60231938	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61426398	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6499253	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6499255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7189424	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7198242	1.00[CEU][hapmap]
rs73579458	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73579497	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8045682	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8046314	1.00[CEU][hapmap]
rs8059345	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9788837	1.00[CEU][hapmap]
rs9889219	0.80[YRI][hapmap]
rs9921045	1.00[CEU][hapmap]

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	nsv906823	chr16:69711533-69959223	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4497676	LOC440348	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:69797400-69821200	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr16:69797600-69816800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr16:69797600-69853400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr16:69797800-69821200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr16:69800600-69817200	Weak transcription	Fetal Stomach	stomach
6	chr16:69800600-69817600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr16:69802800-69821400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr16:69803000-69823400	Weak transcription	Right Ventricle	heart
9	chr16:69803400-69830200	Weak transcription	Fetal Heart	heart
10	chr16:69806800-69817600	Weak transcription	Gastric	stomach
11	chr16:69806800-69821000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr16:69806800-69821200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr16:69806800-69830200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr16:69806800-69833000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr16:69807000-69820800	Weak transcription	Spleen	Spleen
16	chr16:69807000-69821000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr16:69807000-69821400	Weak transcription	Colonic Mucosa	Colon
18	chr16:69807000-69821600	Weak transcription	Stomach Mucosa	stomach
19	chr16:69807000-69821800	Weak transcription	Brain Substantia Nigra	brain
20	chr16:69807000-69822200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr16:69807000-69822400	Weak transcription	Fetal Kidney	kidney
22	chr16:69807000-69830200	Weak transcription	NHDF-Ad	bronchial
23	chr16:69807000-69832000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr16:69807200-69816800	Weak transcription	Placenta	Placenta
25	chr16:69807200-69817200	Weak transcription	Left Ventricle	heart
26	chr16:69807200-69817600	Weak transcription	Esophagus	oesophagus
27	chr16:69807200-69821200	Weak transcription	Brain Angular Gyrus	brain
28	chr16:69807200-69830200	Weak transcription	Osteobl	bone
29	chr16:69807200-69832600	Weak transcription	NHLF	lung
30	chr16:69807200-69832800	Weak transcription	Pancreas	Pancrea
31	chr16:69807200-69852400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr16:69807200-69852800	Weak transcription	Hela-S3	cervix
33	chr16:69807200-69854800	Weak transcription	Psoas Muscle	Psoas
34	chr16:69807400-69816600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr16:69807400-69821400	Weak transcription	Ovary	ovary
36	chr16:69807600-69821200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr16:69807800-69818200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr16:69808000-69833200	Weak transcription	HSMM	muscle
39	chr16:69809200-69821800	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr16:69809600-69816800	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr16:69809600-69820800	Weak transcription	Brain Hippocampus Middle	brain
42	chr16:69809800-69819000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr16:69809800-69821800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr16:69810000-69821200	Weak transcription	Stomach Smooth Muscle	stomach
45	chr16:69810000-69822400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr16:69810000-69839800	Weak transcription	HUVEC	blood vessel
47	chr16:69810200-69817000	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr16:69810200-69817000	Weak transcription	Thymus	Thymus
49	chr16:69810200-69817200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr16:69810200-69817200	Weak transcription	Duodenum Mucosa	Duodenum

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