Variant report

Variant	rs55863174
Chromosome Location	chr16:69819996-69819997
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	chr16:69795431..69797350-chr16:69819161..69821145,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198373	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10048108	0.82[EUR][1000 genomes]
rs10163235	0.82[EUR][1000 genomes]
rs10454066	0.81[EUR][1000 genomes]
rs11075733	0.88[EUR][1000 genomes]
rs11075734	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1139178	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11641521	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11643926	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11644838	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11644914	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12232410	0.80[EUR][1000 genomes]
rs12446201	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12447883	0.81[EUR][1000 genomes]
rs12595869	0.81[EUR][1000 genomes]
rs12596679	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12925371	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1437135	0.84[EUR][1000 genomes]
rs16959035	0.82[EUR][1000 genomes]
rs1800566	0.82[EUR][1000 genomes]
rs1865965	0.81[EUR][1000 genomes]
rs2196574	0.84[EUR][1000 genomes]
rs2361839	0.82[EUR][1000 genomes]
rs3743673	0.82[EUR][1000 genomes]
rs3811349	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4078387	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4341733	0.81[AFR][1000 genomes]
rs4464069	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4497676	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4580150	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4985518	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4985523	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55701476	0.85[EUR][1000 genomes]
rs55992518	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56282083	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57488237	0.82[EUR][1000 genomes]
rs57518557	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57565297	0.81[EUR][1000 genomes]
rs59295369	0.81[EUR][1000 genomes]
rs60231938	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61426398	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6499253	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6499255	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6499257	0.80[AFR][1000 genomes]
rs689455	0.84[EUR][1000 genomes]
rs7186002	0.84[EUR][1000 genomes]
rs7189424	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73579458	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73579497	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74029403	0.80[EUR][1000 genomes]
rs8045682	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8046314	0.80[EUR][1000 genomes]
rs8054096	0.80[EUR][1000 genomes]
rs8059345	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9921045	0.82[EUR][1000 genomes]
rs9933526	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	esv3433379	chr16:69819981-69820393	Weak transcription Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55863174	LOC440348	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 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	chr16:69797600-69853400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr16:69797800-69821200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr16:69802800-69821400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr16:69803000-69823400	Weak transcription	Right Ventricle	heart
6	chr16:69803400-69830200	Weak transcription	Fetal Heart	heart
7	chr16:69806800-69821000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr16:69806800-69821200	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr16:69806800-69830200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr16:69806800-69833000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr16:69807000-69820800	Weak transcription	Spleen	Spleen
12	chr16:69807000-69821000	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr16:69807000-69821400	Weak transcription	Colonic Mucosa	Colon
14	chr16:69807000-69821600	Weak transcription	Stomach Mucosa	stomach
15	chr16:69807000-69821800	Weak transcription	Brain Substantia Nigra	brain
16	chr16:69807000-69822200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr16:69807000-69822400	Weak transcription	Fetal Kidney	kidney
18	chr16:69807000-69830200	Weak transcription	NHDF-Ad	bronchial
19	chr16:69807000-69832000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr16:69807200-69821200	Weak transcription	Brain Angular Gyrus	brain
21	chr16:69807200-69830200	Weak transcription	Osteobl	bone
22	chr16:69807200-69832600	Weak transcription	NHLF	lung
23	chr16:69807200-69832800	Weak transcription	Pancreas	Pancrea
24	chr16:69807200-69852400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr16:69807200-69852800	Weak transcription	Hela-S3	cervix
26	chr16:69807200-69854800	Weak transcription	Psoas Muscle	Psoas
27	chr16:69807400-69821400	Weak transcription	Ovary	ovary
28	chr16:69807600-69821200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr16:69808000-69833200	Weak transcription	HSMM	muscle
30	chr16:69809200-69821800	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr16:69809600-69820800	Weak transcription	Brain Hippocampus Middle	brain
32	chr16:69809800-69821800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr16:69810000-69821200	Weak transcription	Stomach Smooth Muscle	stomach
34	chr16:69810000-69822400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr16:69810000-69839800	Weak transcription	HUVEC	blood vessel
36	chr16:69810200-69820800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr16:69810200-69820800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr16:69810200-69820800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr16:69810200-69820800	Weak transcription	Fetal Muscle Trunk	muscle
40	chr16:69810200-69822200	Weak transcription	Small Intestine	intestine
41	chr16:69810200-69831000	Weak transcription	NHEK	skin
42	chr16:69810200-69833400	Weak transcription	Dnd41	blood
43	chr16:69810400-69820600	Weak transcription	Primary T helper cells PMA-I stimulated	--
44	chr16:69810400-69820800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr16:69810400-69820800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr16:69810400-69821000	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr16:69810400-69821400	Weak transcription	Brain Cingulate Gyrus	brain
48	chr16:69810400-69821600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr16:69810400-69821600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr16:69810400-69830200	Weak transcription	Colon Smooth Muscle	Colon

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