Variant report

Variant	rs3749317
Chromosome Location	chr3:51457035-51457036
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	chr3:51429653..51435090-chr3:51454270..51458499,6	MCF-7	breast:

Extended variants
information (count: 115 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10510757	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10510758	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12485610	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12487426	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12487468	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12489219	0.83[CHD][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs12489414	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12490471	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12490889	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12491048	0.98[ASN][1000 genomes]
rs12492624	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12493265	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12493618	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12493857	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12493978	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12494462	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12494979	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13089799	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13090348	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1370124	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17051783	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17051811	0.89[ASN][1000 genomes]
rs17661242	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17712228	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1842394	0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs2033703	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2061949	0.94[MEX][hapmap]
rs2082992	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2082993	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2101056	0.82[CHB][hapmap]
rs2170177	0.83[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.94[MEX][hapmap];0.80[ASN][1000 genomes]
rs2217938	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2241785	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2304512	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306430	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2306431	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2356261	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2356298	0.94[ASN][1000 genomes]
rs35536327	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3792408	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804766	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828395	0.94[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4468966	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4687553	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4687563	0.91[ASN][1000 genomes]
rs4687601	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687605	0.94[ASN][1000 genomes]
rs4687610	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4687656	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4687691	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4687731	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687777	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687794	0.91[ASN][1000 genomes]
rs4687803	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4687804	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4687811	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4687812	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4687813	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4974096	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4974098	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4974112	0.83[CHD][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs55667499	0.92[ASN][1000 genomes]
rs55671465	0.85[ASN][1000 genomes]
rs56239081	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56729479	0.94[ASN][1000 genomes]
rs57027950	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57047724	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57603251	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57700326	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs57831708	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58059174	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs58189274	0.82[ASN][1000 genomes]
rs58201844	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58568178	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58836277	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59563413	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59838596	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59953568	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60606339	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs61233013	0.91[ASN][1000 genomes]
rs61419317	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61689323	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs72945708	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72945713	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72951443	0.92[ASN][1000 genomes]
rs73834252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73834253	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73834254	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73834258	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73837435	0.94[AFR][1000 genomes]
rs73837437	0.88[AFR][1000 genomes]
rs73837438	0.94[AFR][1000 genomes]
rs73837439	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73837442	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73837443	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs751076	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7642698	0.92[ASN][1000 genomes]
rs880478	0.94[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9817077	0.94[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.89[ASN][1000 genomes]
rs9817872	0.94[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.89[ASN][1000 genomes]
rs9819195	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9820140	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9827186	0.89[ASN][1000 genomes]
rs9829057	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[ASN][1000 genomes]
rs9842600	0.91[ASN][1000 genomes]
rs9843583	0.90[ASN][1000 genomes]
rs9856134	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9861019	0.86[ASN][1000 genomes]
rs9878592	0.83[CHD][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv460536	chr3:51395571-51469107	Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv590276	chr3:51395571-51469107	Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv590277	chr3:51408051-51474418	Strong transcription Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	esv3369762	chr3:51449727-51469314	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv3444499	chr3:51449727-51469614	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51431400-51471200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr3:51432400-51460000	Strong transcription	Liver	Liver
3	chr3:51433400-51477400	Weak transcription	Fetal Heart	heart
4	chr3:51434000-51475600	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr3:51434200-51460200	Strong transcription	Dnd41	blood
6	chr3:51434200-51477600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:51434400-51457200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:51434600-51471000	Weak transcription	Stomach Mucosa	stomach
9	chr3:51435200-51478000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:51435600-51460200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:51436600-51461000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:51436800-51461000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:51437800-51460000	Strong transcription	Duodenum Mucosa	Duodenum
14	chr3:51439800-51478000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:51440000-51460200	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr3:51440800-51478200	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr3:51441000-51460200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr3:51441600-51461400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr3:51444000-51460600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr3:51444000-51461200	Strong transcription	Placenta	Placenta
21	chr3:51444800-51460000	Strong transcription	Primary T cells from cord blood	blood
22	chr3:51444800-51477800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr3:51445400-51460400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:51445400-51478400	Strong transcription	Primary B cells from peripheral blood	blood
25	chr3:51445600-51460200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:51445600-51460400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr3:51445800-51460000	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr3:51445800-51460000	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr3:51445800-51460200	Strong transcription	Adipose Nuclei	Adipose
30	chr3:51446000-51458800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr3:51446000-51459400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr3:51446000-51460600	Strong transcription	Fetal Thymus	thymus
33	chr3:51446000-51460800	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr3:51446200-51458400	Strong transcription	Primary hematopoietic stem cells	blood
35	chr3:51446200-51458400	Strong transcription	Lung	lung
36	chr3:51446200-51458600	Strong transcription	Sigmoid Colon	Sigmoid Colon
37	chr3:51446200-51460200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr3:51446200-51460400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr3:51446200-51460400	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr3:51446200-51460600	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr3:51446200-51471000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:51446400-51458400	Strong transcription	Brain Inferior Temporal Lobe	brain
43	chr3:51446400-51458600	Strong transcription	Fetal Muscle Leg	muscle
44	chr3:51446400-51459200	Strong transcription	Left Ventricle	heart
45	chr3:51446400-51460000	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr3:51446400-51460000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr3:51446400-51461000	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr3:51446400-51461200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr3:51446400-51461200	Strong transcription	Fetal Muscle Trunk	muscle
50	chr3:51446400-51461200	Strong transcription	Thymus	Thymus

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