Variant report

Variant	rs12486835
Chromosome Location	chr3:194979407-194979408
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:194976111..194979050-chr3:194979100..194980799,3	K562	blood:
2	chr3:194835818..194838322-chr3:194977897..194980111,2	K562	blood:
3	chr3:194391105..194394740-chr3:194978001..194983059,6	K562	blood:
4	chr3:194391105..194394913-chr3:194978195..194983059,8	K562	blood:
5	chr3:194604268..194606263-chr3:194979246..194980767,2	K562	blood:
6	chr3:194391338..194394137-chr3:194977296..194982165,5	MCF-7	breast:
7	chr3:194979343..194985907-chr3:194989595..194992143,7	K562	blood:
8	chr3:194471513..194474254-chr3:194977956..194979790,2	K562	blood:
9	chr3:194979343..194983092-chr3:194989595..194993137,5	K562	blood:
10	chr3:194967605..194970943-chr3:194977628..194981159,3	K562	blood:
11	chr3:194334694..194337644-chr3:194979245..194981066,2	K562	blood:
12	chr3:194874240..194875817-chr3:194979341..194981767,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000173950	Chromatin interaction
ENSG00000145014	Chromatin interaction
ENSG00000041802	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	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10933703	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11917438	0.81[AFR][1000 genomes];0.92[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];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11921174	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12486168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486220	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]
rs12486636	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs12486805	1.00[CHB][hapmap]
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]
rs2029707	1.00[CHB][hapmap]
rs2050807	1.00[CHB][hapmap]
rs35899174	0.85[EUR][1000 genomes]
rs3796161	1.00[CHB][hapmap]
rs56281422	0.85[EUR][1000 genomes]
rs58113840	1.00[ASN][1000 genomes]
rs59579668	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60677730	0.85[EUR][1000 genomes]
rs6437466	0.97[AFR][1000 genomes];0.92[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[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7653179	1.00[CHB][hapmap]
rs999331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.89[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:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194957400-194979800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:194959200-194979600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:194965200-194979600	Weak transcription	Right Atrium	heart
4	chr3:194966600-194980000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr3:194967800-194980000	Weak transcription	Dnd41	blood
6	chr3:194968000-194979800	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr3:194969200-194979600	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr3:194972200-194979600	Weak transcription	Thymus	Thymus
9	chr3:194974200-194979600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:194974200-194979600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:194974200-194979600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:194974200-194979600	Weak transcription	Osteobl	bone
13	chr3:194974200-194980000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr3:194975200-194979600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:194975400-194980000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:194976200-194979600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr3:194976200-194979800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:194976400-194980200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:194976800-194979800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:194977200-194979800	Weak transcription	Esophagus	oesophagus
21	chr3:194977400-194980000	Enhancers	Brain Cingulate Gyrus	brain
22	chr3:194977600-194980000	Enhancers	Fetal Thymus	thymus
23	chr3:194977800-194980200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:194978000-194979600	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr3:194978000-194980000	Enhancers	Fetal Stomach	stomach
26	chr3:194978000-194980200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:194978200-194979600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr3:194978200-194979800	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr3:194978200-194979800	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr3:194978200-194980000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr3:194978200-194980000	Enhancers	Brain Hippocampus Middle	brain
32	chr3:194978400-194979800	Enhancers	GM12878-XiMat	blood
33	chr3:194978400-194980000	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr3:194978400-194980000	Enhancers	Brain Angular Gyrus	brain
35	chr3:194978400-194980000	Enhancers	Fetal Muscle Leg	muscle
36	chr3:194978400-194980000	Enhancers	Right Ventricle	heart
37	chr3:194978400-194980000	Enhancers	Hela-S3	cervix
38	chr3:194978400-194980200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr3:194978400-194980400	Enhancers	Placenta	Placenta
40	chr3:194978600-194979600	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr3:194978600-194979600	Enhancers	Brain Substantia Nigra	brain
42	chr3:194978600-194979600	Enhancers	Fetal Lung	lung
43	chr3:194978600-194979600	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr3:194978600-194979600	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr3:194978600-194979600	Enhancers	HepG2	liver
46	chr3:194978600-194979800	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr3:194978600-194980000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:194978600-194980000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr3:194978600-194980000	Enhancers	Brain Anterior Caudate	brain
50	chr3:194978600-194980000	Enhancers	Brain Germinal Matrix	brain

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