Variant report

Variant	rs3749748
Chromosome Location	chr5:127350549-127350550
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	chr5:127350306..127352684-chr5:127415798..127418710,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000245937	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1112956	1.00[ASW][hapmap];0.94[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11948128	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17764730	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1993878	0.94[CEU][hapmap];0.94[JPT][hapmap]
rs2250127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2409110	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2568928	1.00[ASW][hapmap];0.94[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.93[MKK][hapmap];0.90[TSI][hapmap]
rs2617617	0.81[ASN][1000 genomes]
rs34576922	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6860245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6888037	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6889311	0.94[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7734927	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs790154	1.00[ASW][hapmap];0.87[CEU][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap]
rs790155	1.00[ASW][hapmap];0.87[CEU][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap]
rs9327468	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1813981	chr5:127327649-127437401	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	esv1806594	chr5:127336033-127410767	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv1808488	chr5:127336033-127410767	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv1825228	chr5:127336033-127410767	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	esv1829119	chr5:127336033-127410767	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3749748	CTC-228N24.3	cis	Skin Sun Exposed Lower leg	GTEx
rs3749748	FBN2	cis	cerebellum	SCAN
rs3749748	CTC-228N24.3	cis	Muscle Skeletal	GTEx
rs3749748	CTC-228N24.3	cis	Thyroid	GTEx
rs3749748	FLJ33630	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127297800-127358400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr5:127324400-127354800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr5:127324400-127358400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr5:127326400-127359400	Weak transcription	GM12878-XiMat	blood
5	chr5:127327800-127359400	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr5:127328200-127379800	Weak transcription	Esophagus	oesophagus
7	chr5:127329400-127351600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr5:127332400-127388800	Weak transcription	Aorta	Aorta
9	chr5:127333600-127354200	Weak transcription	Left Ventricle	heart
10	chr5:127333600-127358200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr5:127333600-127358400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr5:127333600-127388800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr5:127333600-127417800	Weak transcription	Pancreas	Pancrea
14	chr5:127333800-127370800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr5:127334600-127394000	Weak transcription	Lung	lung
16	chr5:127335000-127355800	Weak transcription	Primary T cells from cord blood	blood
17	chr5:127335000-127397600	Weak transcription	NHDF-Ad	bronchial
18	chr5:127336800-127375000	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr5:127338400-127355800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr5:127338600-127358400	Weak transcription	HMEC	breast
21	chr5:127338600-127359400	Weak transcription	Ovary	ovary
22	chr5:127339000-127354600	Weak transcription	Primary B cells from cord blood	blood
23	chr5:127341800-127356000	Weak transcription	Psoas Muscle	Psoas
24	chr5:127342000-127358600	Weak transcription	Fetal Muscle Leg	muscle
25	chr5:127343000-127380000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr5:127343800-127361600	Weak transcription	Adipose Nuclei	Adipose
27	chr5:127345400-127355800	Weak transcription	Gastric	stomach
28	chr5:127345400-127357600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr5:127345600-127371400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr5:127345800-127351000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr5:127347000-127358400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr5:127347400-127362200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr5:127347800-127365800	Weak transcription	Duodenum Mucosa	Duodenum
34	chr5:127349400-127357600	Weak transcription	Osteobl	bone
35	chr5:127349800-127352600	Enhancers	HUVEC	blood vessel
36	chr5:127349800-127352800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr5:127350000-127350600	Enhancers	Small Intestine	intestine
38	chr5:127350400-127350600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr5:127350400-127350600	Enhancers	Brain Hippocampus Middle	brain
40	chr5:127350400-127350600	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr5:127350400-127350600	Enhancers	Brain Substantia Nigra	brain
42	chr5:127350400-127350600	Enhancers	Right Atrium	heart
43	chr5:127350400-127350600	Enhancers	Spleen	Spleen
44	chr5:127350400-127350600	Enhancers	A549	lung
45	chr5:127350400-127350800	Enhancers	Stomach Mucosa	stomach
46	chr5:127350400-127351200	Enhancers	HSMMtube	muscle
47	chr5:127350400-127358400	Weak transcription	HSMM	muscle

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