Variant report

Variant	rs12461130
Chromosome Location	chr19:56785028-56785029
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	chr19:56750344..56752392-chr19:56783866..56786080,2	K562	blood:

Variant related genes	Relation type
ENSG00000267908	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10775568	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11084440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11667369	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11670857	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11670870	0.81[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11672079	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11672081	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11672220	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11673002	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11883295	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12460523	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17273365	0.85[CEU][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2869158	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3205192	0.85[CEU][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57090480	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57731201	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58815584	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59503198	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59565427	0.91[EUR][1000 genomes]
rs59820036	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62122532	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62122534	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62122536	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7247765	0.84[JPT][hapmap]
rs7252570	0.85[CEU][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73069662	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs755058	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs758758	0.85[CEU][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs758760	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8101809	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8103418	0.85[CEU][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8104291	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs965567	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064371	chr19:56418215-56842450	ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
2	nsv1057316	chr19:56418215-56849458	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
3	nsv912516	chr19:56601298-56981382	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers 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	93 gene(s)	inside rSNPs	diseases
4	nsv1058152	chr19:56703368-56805035	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv544093	chr19:56703368-56805035	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv526325	chr19:56741186-56852035	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv949121	chr19:56754719-57591038	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
8	nsv528817	chr19:56779041-56785408	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56729200-56803000	Weak transcription	Pancreas	Pancrea
2	chr19:56753000-56809000	Weak transcription	Gastric	stomach
3	chr19:56764200-56788400	Weak transcription	A549	lung
4	chr19:56764400-56788400	Weak transcription	Fetal Muscle Leg	muscle
5	chr19:56764400-56788600	Weak transcription	Duodenum Mucosa	Duodenum
6	chr19:56764400-56798600	Weak transcription	Placenta	Placenta
7	chr19:56764600-56788200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr19:56764600-56799400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr19:56764600-56804000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr19:56765000-56788400	Weak transcription	Brain Anterior Caudate	brain
11	chr19:56766600-56804200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr19:56768600-56794800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr19:56769200-56788400	Weak transcription	Adipose Nuclei	Adipose
14	chr19:56770200-56795200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr19:56770200-56799400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr19:56770400-56804400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr19:56771200-56787200	Weak transcription	Liver	Liver
18	chr19:56771200-56788400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr19:56771200-56792000	Weak transcription	Aorta	Aorta
20	chr19:56771400-56817200	Weak transcription	Fetal Brain Male	brain
21	chr19:56771600-56807000	Weak transcription	Right Ventricle	heart
22	chr19:56772000-56788400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr19:56772400-56788400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr19:56772800-56788400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr19:56772800-56807600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr19:56772800-56824200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr19:56773000-56788200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr19:56773000-56807400	Weak transcription	Esophagus	oesophagus
29	chr19:56773600-56790000	Weak transcription	Primary B cells from cord blood	blood
30	chr19:56774200-56788400	Weak transcription	Fetal Muscle Trunk	muscle
31	chr19:56775800-56815600	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr19:56777000-56792800	Weak transcription	Fetal Intestine Large	intestine
33	chr19:56779600-56820200	Weak transcription	Hela-S3	cervix
34	chr19:56779800-56800000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr19:56779800-56807200	Weak transcription	Left Ventricle	heart
36	chr19:56781400-56804600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr19:56782200-56799200	Weak transcription	Fetal Intestine Small	intestine
38	chr19:56782400-56788400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr19:56782600-56786800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr19:56782600-56794200	Weak transcription	K562	blood
41	chr19:56782800-56788400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr19:56782800-56788400	Weak transcription	Fetal Kidney	kidney
43	chr19:56782800-56788400	Weak transcription	HSMMtube	muscle
44	chr19:56782800-56825200	Weak transcription	Psoas Muscle	Psoas
45	chr19:56783000-56788200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr19:56783000-56825000	Weak transcription	Stomach Mucosa	stomach
47	chr19:56783200-56804000	Weak transcription	Brain Germinal Matrix	brain
48	chr19:56783200-56805400	Weak transcription	Brain Hippocampus Middle	brain
49	chr19:56783400-56785400	Enhancers	Osteobl	bone
50	chr19:56783400-56794000	Weak transcription	Primary monocytes fromperipheralblood	blood

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