Variant report

Variant	rs3012124
Chromosome Location	chr13:49626991-49626992
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1407826	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1937182	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1983806	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2181906	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2987534	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3012130	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3012134	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942806	0.90[ASN][1000 genomes]
rs4942807	1.00[AMR][1000 genomes]
rs57277286	1.00[AMR][1000 genomes]
rs57590763	1.00[AMR][1000 genomes]
rs58064396	1.00[AMR][1000 genomes]
rs58372993	1.00[AMR][1000 genomes]
rs61192069	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6561495	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561498	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561508	1.00[AMR][1000 genomes]
rs7326409	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7338704	1.00[CHB][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7999767	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs912193	0.85[ASN][1000 genomes]
rs928039	1.00[ASN][1000 genomes]
rs9316432	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv455882	chr13:49531551-49679157	Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv561593	chr13:49531551-49679157	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	esv1793883	chr13:49543723-49789164	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	esv1803100	chr13:49576474-49655941	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49551400-49638800	Weak transcription	Pancreas	Pancrea
2	chr13:49568800-49627000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr13:49573400-49634800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr13:49582200-49659000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr13:49584200-49649200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr13:49592800-49649600	Weak transcription	Fetal Intestine Large	intestine
7	chr13:49594800-49636000	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr13:49598000-49650200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr13:49599000-49649200	Weak transcription	Primary B cells from peripheral blood	blood
10	chr13:49601800-49660600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr13:49603200-49649200	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr13:49603200-49652200	Weak transcription	Dnd41	blood
13	chr13:49604800-49636400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr13:49605200-49643400	Weak transcription	HSMM	muscle
15	chr13:49607800-49627000	Weak transcription	HMEC	breast
16	chr13:49608800-49638800	Weak transcription	Ovary	ovary
17	chr13:49608800-49658800	Weak transcription	Duodenum Mucosa	Duodenum
18	chr13:49612600-49628600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr13:49612800-49627000	Weak transcription	Lung	lung
20	chr13:49612800-49627400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr13:49614600-49628400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr13:49618600-49636000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr13:49619400-49628600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr13:49620600-49636200	Weak transcription	Primary T cells from cord blood	blood
25	chr13:49623000-49627000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr13:49624200-49628800	Weak transcription	Fetal Stomach	stomach
27	chr13:49625200-49628000	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr13:49625600-49631200	Weak transcription	GM12878-XiMat	blood
29	chr13:49625600-49636600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr13:49625600-49642600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr13:49625800-49627600	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr13:49625800-49631400	Weak transcription	Primary hematopoietic stem cells	blood
33	chr13:49626000-49627200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr13:49626000-49628600	Weak transcription	Primary B cells from cord blood	blood
35	chr13:49626000-49636200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr13:49626200-49650200	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr13:49626400-49628200	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr13:49626600-49627400	Strong transcription	Fetal Intestine Small	intestine
39	chr13:49626600-49627600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr13:49626600-49627600	Flanking Active TSS	Hela-S3	cervix
41	chr13:49626600-49628600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr13:49626600-49628600	Enhancers	NHEK	skin
43	chr13:49626600-49628800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr13:49626600-49629200	Enhancers	Placenta	Placenta
45	chr13:49626800-49627000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr13:49626800-49627200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr13:49626800-49627200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr13:49626800-49627200	Enhancers	Osteobl	bone
49	chr13:49626800-49627400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr13:49626800-49627400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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