Variant report

Variant	rs17800749
Chromosome Location	chr2:134003754-134003755
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	chr2:134003474..134006247-chr2:134007339..134011249,3	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10167342	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10170384	0.83[AMR][1000 genomes]
rs10182118	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10185165	0.83[AMR][1000 genomes]
rs10189529	0.82[AMR][1000 genomes]
rs10193871	1.00[ASW][hapmap];0.81[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10206544	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10210486	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10496702	0.81[CEU][hapmap];0.87[GIH][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes]
rs10496703	0.82[AMR][1000 genomes]
rs10496704	0.87[MEX][hapmap];0.82[AMR][1000 genomes]
rs12464930	0.81[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12469282	0.87[MEX][hapmap];0.84[AMR][1000 genomes]
rs13390487	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13391016	0.83[AMR][1000 genomes]
rs13399345	0.81[CHB][hapmap];0.82[CHD][hapmap];0.87[MEX][hapmap];0.82[AMR][1000 genomes]
rs13399558	0.81[CHB][hapmap];0.82[CHD][hapmap];0.87[MEX][hapmap];0.82[AMR][1000 genomes]
rs13412008	0.87[MEX][hapmap];0.82[AMR][1000 genomes]
rs13413333	1.00[ASW][hapmap];0.81[CEU][hapmap];0.83[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13414129	0.92[ASN][1000 genomes]
rs13418981	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13430905	0.81[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13431418	0.81[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1344725	0.83[AMR][1000 genomes]
rs1344727	0.81[AMR][1000 genomes]
rs1344728	0.81[AMR][1000 genomes]
rs1430169	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1820927	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1835341	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2115865	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2217428	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4057049	0.81[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4589811	0.87[MEX][hapmap];0.82[AMR][1000 genomes]
rs62178459	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62179960	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62179961	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62179967	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62179969	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62179970	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62180003	0.80[AMR][1000 genomes]
rs6430405	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6744863	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6749561	0.87[CHB][hapmap];0.87[CHD][hapmap];0.91[ASN][1000 genomes]
rs6756852	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7568471	0.82[ASN][1000 genomes]
rs7600407	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7600871	0.81[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7603759	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949629	chr2:133830379-134014961	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv1001601	chr2:133838626-134005959	Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv997821	chr2:133868822-134360220	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv535927	chr2:133868822-134360220	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv1002488	chr2:133890159-134275312	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv535928	chr2:133890159-134275312	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv1011100	chr2:133900062-134046163	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	esv3375790	chr2:133906915-134222833	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv1005405	chr2:133930876-134055434	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv535929	chr2:133930876-134055434	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv516915	chr2:133999831-134054662	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:133991600-134005400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:133994000-134023600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:133998400-134005000	Weak transcription	Psoas Muscle	Psoas
4	chr2:133998400-134005800	Weak transcription	Left Ventricle	heart
5	chr2:133998600-134003800	Weak transcription	Brain Angular Gyrus	brain
6	chr2:133998800-134004600	Weak transcription	Fetal Heart	heart
7	chr2:133998800-134013000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:133998800-134014800	Weak transcription	Fetal Stomach	stomach
9	chr2:133999000-134005000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:133999200-134005400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr2:133999200-134007800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:133999400-134003800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:133999400-134005200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr2:133999400-134005200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr2:133999400-134005200	Weak transcription	Fetal Muscle Leg	muscle
16	chr2:133999400-134005400	Weak transcription	Ovary	ovary
17	chr2:133999400-134005800	Weak transcription	Lung	lung
18	chr2:134000200-134005400	Weak transcription	NHLF	lung
19	chr2:134001200-134005200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:134001200-134005800	Weak transcription	Right Ventricle	heart
21	chr2:134002200-134004800	Weak transcription	HMEC	breast
22	chr2:134003200-134004600	Enhancers	Fetal Brain Male	brain
23	chr2:134003400-134003800	Enhancers	Brain Hippocampus Middle	brain
24	chr2:134003600-134003800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr2:134003600-134003800	Enhancers	Brain Anterior Caudate	brain
26	chr2:134003600-134004600	Enhancers	Fetal Brain Female	brain
27	chr2:134003600-134006000	Enhancers	Fetal Lung	lung
28	chr2:134003600-134006400	Enhancers	Brain Substantia Nigra	brain

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