Variant report

Variant	rs12466032
Chromosome Location	chr2:73839309-73839310
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	chr2:73837883..73840443-chr2:74211046..74212867,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235499	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10192708	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10496189	1.00[ASN][1000 genomes]
rs11884364	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11890811	1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11900562	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12475442	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12475618	1.00[ASN][1000 genomes]
rs12476993	1.00[JPT][hapmap]
rs12477496	0.80[AMR][1000 genomes]
rs12479158	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12479243	1.00[ASN][1000 genomes]
rs1320374	0.88[YRI][hapmap]
rs1358452	1.00[ASN][1000 genomes]
rs1403283	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17009036	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17009051	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17009061	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17009070	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17009339	1.00[JPT][hapmap]
rs17848867	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1881244	1.00[ASN][1000 genomes]
rs2140194	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2421583	0.84[YRI][hapmap]
rs28730853	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2901451	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34617744	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34735981	1.00[ASN][1000 genomes]
rs36057913	1.00[ASN][1000 genomes]
rs55745821	0.80[AMR][1000 genomes]
rs60130127	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61335053	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6706333	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6708480	1.00[ASN][1000 genomes]
rs6711285	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6718672	1.00[ASN][1000 genomes]
rs6723002	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6723245	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6725385	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6732440	0.88[YRI][hapmap]
rs6734298	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6735139	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6737693	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6746054	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6751876	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6752342	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6752620	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6759120	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72635973	1.00[ASN][1000 genomes]
rs7558613	1.00[ASN][1000 genomes]
rs7567443	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7570683	0.83[YRI][hapmap]
rs7571147	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7574950	1.00[ASN][1000 genomes]
rs7577699	1.00[ASN][1000 genomes]
rs7587537	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7599369	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7600935	1.00[ASN][1000 genomes]
rs7603754	1.00[ASN][1000 genomes]
rs7608706	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428051	chr2:73717032-74030067	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2757806	chr2:73717032-74078592	Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv2759060	chr2:73717032-74078592	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS 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	36 gene(s)	inside rSNPs	diseases
4	nsv874267	chr2:73717656-73857002	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv1013385	chr2:73822056-74041441	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv874268	chr2:73837751-73907696	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv874269	chr2:73837751-73914019	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv874270	chr2:73837751-73916672	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv10013	chr2:73838181-73841175	Enhancers Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73801000-73844000	Weak transcription	Fetal Kidney	kidney
2	chr2:73822600-73840800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:73823000-73844600	Weak transcription	Primary B cells from cord blood	blood
4	chr2:73826000-73841200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:73826200-73841400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr2:73827000-73840600	Weak transcription	NHLF	lung
7	chr2:73827800-73840400	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr2:73829000-73839400	Weak transcription	Placenta	Placenta
9	chr2:73829200-73840000	Weak transcription	Primary hematopoietic stem cells	blood
10	chr2:73829400-73845400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr2:73829600-73840200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr2:73829800-73839600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr2:73829800-73840000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr2:73829800-73840000	Weak transcription	Gastric	stomach
15	chr2:73829800-73840400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:73830000-73840800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr2:73830400-73843600	Weak transcription	Aorta	Aorta
18	chr2:73830600-73839600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr2:73830600-73840000	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr2:73830600-73841200	Weak transcription	Liver	Liver
21	chr2:73830600-73843000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:73830600-73847600	Weak transcription	Spleen	Spleen
23	chr2:73830600-73854800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr2:73830800-73840800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr2:73831000-73842200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr2:73831200-73839600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr2:73831200-73841200	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:73836200-73839800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr2:73836400-73839600	Weak transcription	HSMM	muscle
30	chr2:73836400-73844200	Weak transcription	Adipose Nuclei	Adipose
31	chr2:73836400-73852600	Weak transcription	Ovary	ovary
32	chr2:73836800-73839800	Weak transcription	Fetal Intestine Large	intestine
33	chr2:73837400-73845000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:73837800-73839600	Strong transcription	Brain Substantia Nigra	brain
35	chr2:73837800-73839600	Enhancers	Thymus	Thymus
36	chr2:73838000-73839400	Strong transcription	Primary T cells from cord blood	blood
37	chr2:73838000-73845200	Weak transcription	Brain Hippocampus Middle	brain
38	chr2:73838200-73843200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:73838400-73839600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:73838400-73840000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:73838400-73840200	Weak transcription	Fetal Muscle Trunk	muscle
42	chr2:73838400-73841800	Weak transcription	Left Ventricle	heart
43	chr2:73838400-73842200	Weak transcription	Brain Anterior Caudate	brain
44	chr2:73838400-73844200	Weak transcription	Fetal Lung	lung
45	chr2:73838400-73844200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr2:73838400-73852600	Weak transcription	Right Ventricle	heart
47	chr2:73838600-73841000	Weak transcription	GM12878-XiMat	blood
48	chr2:73838600-73842200	Weak transcription	Duodenum Mucosa	Duodenum
49	chr2:73838600-73843800	Weak transcription	Lung	lung
50	chr2:73838600-73845200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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