Variant report

Variant	rs55657471
Chromosome Location	chr3:121456225-121456226
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	chr3:121456187..121459032-chr3:121465141..121468523,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173230	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11706783	0.81[ASN][1000 genomes]
rs11707504	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11707518	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11707716	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11714406	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11715951	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11716984	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11719093	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11719458	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11720859	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11721318	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13061326	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13062684	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13072618	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13072767	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13074834	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13077135	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13083794	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13087578	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13090660	0.80[EUR][1000 genomes]
rs13090798	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13433692	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13434284	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1573819	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17691170	0.83[EUR][1000 genomes]
rs2070180	0.82[EUR][1000 genomes]
rs28660600	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28674947	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs33988592	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34086988	0.82[EUR][1000 genomes]
rs34667636	0.82[EUR][1000 genomes]
rs35679661	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35988617	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36142735	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3732408	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4280673	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4298081	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4311252	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4413346	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55643643	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56314138	0.82[EUR][1000 genomes]
rs62268732	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62268734	0.88[ASN][1000 genomes]
rs66653099	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6768621	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6776670	0.81[ASN][1000 genomes]
rs6784571	0.81[ASN][1000 genomes]
rs6789736	0.81[ASN][1000 genomes]
rs6791046	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7427165	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9289177	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9812228	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9816844	0.82[EUR][1000 genomes]
rs9822949	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9839617	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9841595	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9878086	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9883467	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv432480	chr3:121355723-121629928	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv432482	chr3:121364236-121629634	Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv432481	chr3:121364236-121637178	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv829703	chr3:121383290-121534493	Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	nsv516233	chr3:121419301-121670405	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' 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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs55657471	IQCB1	cis	Whole Blood	GTEx
rs55657471	IQCB1	Cis_1M	lymphoblastoid	RTeQTL
rs55657471	HCLS1	cis	Whole Blood	GTEx
rs55657471	SLC15A2	Cis_1M	lymphoblastoid	RTeQTL
rs55657471	EAF2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121436600-121466600	Weak transcription	Stomach Mucosa	stomach
2	chr3:121439400-121467200	Weak transcription	Small Intestine	intestine
3	chr3:121443400-121464800	Weak transcription	Fetal Brain Male	brain
4	chr3:121444600-121466400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:121444800-121457200	Weak transcription	Gastric	stomach
6	chr3:121444800-121457200	Weak transcription	Right Ventricle	heart
7	chr3:121444800-121457400	Weak transcription	Pancreas	Pancrea
8	chr3:121444800-121458800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr3:121444800-121458800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:121444800-121466400	Weak transcription	Colonic Mucosa	Colon
11	chr3:121444800-121467200	Weak transcription	Aorta	Aorta
12	chr3:121444800-121467400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:121444800-121467400	Weak transcription	Spleen	Spleen
14	chr3:121445200-121457200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:121445200-121457800	Weak transcription	Lung	lung
16	chr3:121445200-121466200	Weak transcription	Fetal Intestine Small	intestine
17	chr3:121445200-121466800	Weak transcription	Thymus	Thymus
18	chr3:121445200-121467400	Weak transcription	Esophagus	oesophagus
19	chr3:121445800-121467000	Weak transcription	Fetal Stomach	stomach
20	chr3:121445800-121467400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr3:121447400-121456800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr3:121447600-121467000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr3:121447800-121466400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr3:121447800-121467000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr3:121448000-121457800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr3:121448000-121466400	Weak transcription	Colon Smooth Muscle	Colon
27	chr3:121448000-121466400	Weak transcription	Fetal Kidney	kidney
28	chr3:121448200-121458400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr3:121448200-121458800	Weak transcription	Dnd41	blood
30	chr3:121448200-121466600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr3:121448400-121466400	Weak transcription	HSMM	muscle
32	chr3:121448400-121466800	Weak transcription	Hela-S3	cervix
33	chr3:121448600-121458800	Weak transcription	Adipose Nuclei	Adipose
34	chr3:121448600-121466400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:121448800-121457400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:121448800-121457800	Weak transcription	Stomach Smooth Muscle	stomach
37	chr3:121448800-121458800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr3:121448800-121459200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr3:121448800-121460000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr3:121448800-121460400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr3:121448800-121463600	Weak transcription	Ovary	ovary
42	chr3:121448800-121464600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr3:121448800-121465600	Weak transcription	HUVEC	blood vessel
44	chr3:121448800-121466400	Weak transcription	Fetal Lung	lung
45	chr3:121448800-121466400	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr3:121448800-121466800	Weak transcription	Primary hematopoietic stem cells	blood
47	chr3:121448800-121467400	Weak transcription	Fetal Muscle Trunk	muscle
48	chr3:121448800-121467400	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr3:121449000-121458800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr3:121449000-121464800	Weak transcription	Primary T helper cells PMA-I stimulated	--

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