Variant report

Variant	rs12486220
Chromosome Location	chr3:194975720-194975721
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:194971128..194973869-chr3:194974801..194977489,3	MCF-7	breast:
2	chr3:194969929..194972409-chr3:194974266..194976627,2	K562	blood:
3	chr3:194966215..194969302-chr3:194974051..194976672,3	K562	blood:
4	chr3:194975706..194977223-chr3:194978127..194981096,2	MCF-7	breast:
5	chr3:194974867..194977335-chr3:194981493..194983475,2	K562	blood:
6	chr3:194971855..194976497-chr3:194977999..194982150,7	K562	blood:

Variant related genes	Relation type
ENSG00000173950	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10933702	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10933703	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11917438	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11918143	0.85[EUR][1000 genomes]
rs11919965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11921174	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12486168	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486636	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs12486805	1.00[CHB][hapmap]
rs12486835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12487670	1.00[CHB][hapmap]
rs12488616	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12488979	1.00[CHB][hapmap]
rs12489090	1.00[CHB][hapmap]
rs12490460	1.00[CHB][hapmap]
rs12490658	1.00[CHB][hapmap]
rs12491026	1.00[CHB][hapmap]
rs12491371	1.00[CHB][hapmap]
rs12491808	1.00[CHB][hapmap]
rs12491854	1.00[CHB][hapmap]
rs12492289	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492552	1.00[CHB][hapmap]
rs12492644	0.95[EUR][1000 genomes]
rs12494306	0.85[EUR][1000 genomes]
rs12494759	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12494773	1.00[CHB][hapmap]
rs12494820	0.88[CHB][hapmap]
rs12496628	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12497444	0.85[EUR][1000 genomes]
rs12497478	1.00[CHB][hapmap]
rs12497906	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap]
rs2029707	1.00[CHB][hapmap]
rs2050807	1.00[CHB][hapmap]
rs35899174	0.85[EUR][1000 genomes]
rs3796161	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs56281422	0.85[EUR][1000 genomes]
rs58113840	1.00[ASN][1000 genomes]
rs59579668	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60677730	0.85[EUR][1000 genomes]
rs6437466	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66510151	1.00[ASN][1000 genomes]
rs67388686	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67413252	0.81[EUR][1000 genomes]
rs67484513	1.00[ASN][1000 genomes]
rs6767801	1.00[CHB][hapmap]
rs6777904	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6785108	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790425	0.85[EUR][1000 genomes]
rs6798243	1.00[CHB][hapmap]
rs6804467	1.00[CHB][hapmap];0.95[EUR][1000 genomes]
rs73069019	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs755202	1.00[CHB][hapmap]
rs7642127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7653179	1.00[CHB][hapmap]
rs999331	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007697	chr3:194554814-195009930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536873	chr3:194554814-195009930	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1014826	chr3:194834615-195631793	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
5	nsv536876	chr3:194834615-195631793	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
6	nsv533904	chr3:194868329-195438728	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
7	nsv1010168	chr3:194874494-195135790	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv536877	chr3:194874494-195135790	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking 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	21 gene(s)	inside rSNPs	diseases
9	nsv997956	chr3:194879534-195087539	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv536878	chr3:194879534-195087539	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
11	esv1832781	chr3:194902818-195528226	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
12	nsv432508	chr3:194916131-195478861	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases
13	nsv432510	chr3:194935314-195478861	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases
14	nsv984539	chr3:194945800-194984579	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
15	nsv1005519	chr3:194964301-195340515	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194957400-194979800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:194958400-194979400	Weak transcription	K562	blood
3	chr3:194959200-194979600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:194960000-194978600	Weak transcription	Brain Substantia Nigra	brain
5	chr3:194961600-194978600	Weak transcription	HUVEC	blood vessel
6	chr3:194961600-194979400	Weak transcription	Pancreas	Pancrea
7	chr3:194961800-194978800	Weak transcription	Lung	lung
8	chr3:194962000-194977800	Weak transcription	Right Ventricle	heart
9	chr3:194962000-194978800	Weak transcription	Gastric	stomach
10	chr3:194962600-194979400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:194965200-194979600	Weak transcription	Right Atrium	heart
12	chr3:194966600-194978600	Weak transcription	HepG2	liver
13	chr3:194966600-194980000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr3:194967800-194980000	Weak transcription	Dnd41	blood
15	chr3:194968000-194976000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:194968000-194979800	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr3:194968200-194979400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr3:194968400-194975800	Weak transcription	Fetal Brain Female	brain
19	chr3:194969200-194979600	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr3:194970800-194977000	Enhancers	Fetal Muscle Leg	muscle
21	chr3:194972000-194979000	Weak transcription	Fetal Heart	heart
22	chr3:194972200-194976200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:194972200-194976600	Weak transcription	Spleen	Spleen
24	chr3:194972200-194979600	Weak transcription	Thymus	Thymus
25	chr3:194972400-194976200	Weak transcription	Placenta	Placenta
26	chr3:194972600-194978600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr3:194972600-194979200	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr3:194972600-194979400	Weak transcription	Primary T cells from cord blood	blood
29	chr3:194973400-194977000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr3:194973600-194977200	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr3:194974000-194976400	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr3:194974000-194976400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr3:194974000-194976600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr3:194974000-194977000	Weak transcription	Hela-S3	cervix
35	chr3:194974000-194977200	Enhancers	H1 Cell Line	embryonic stem cell
36	chr3:194974000-194978200	Weak transcription	Rectal Smooth Muscle	rectum
37	chr3:194974000-194978600	Weak transcription	Primary hematopoietic stem cells	blood
38	chr3:194974000-194978600	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr3:194974000-194978800	Weak transcription	Fetal Brain Male	brain
40	chr3:194974000-194978800	Weak transcription	NH-A	brain
41	chr3:194974000-194979200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:194974200-194976200	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr3:194974200-194976400	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr3:194974200-194976600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr3:194974200-194977200	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr3:194974200-194977400	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr3:194974200-194978200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:194974200-194978600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr3:194974200-194978600	Weak transcription	Brain Anterior Caudate	brain
50	chr3:194974200-194978600	Weak transcription	Duodenum Smooth Muscle	Duodenum

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