Variant report

Variant	rs3013640
Chromosome Location	chr13:30086927-30086928
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:30086183..30088447-chr13:30100578..30102906,2	K562	blood:
2	chr13:30086595..30089289-chr13:30090102..30093020,2	K562	blood:
3	chr13:30085195..30087223-chr13:30096814..30099566,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1018680	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1124594	1.00[ASN][1000 genomes]
rs12427581	1.00[ASW][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.81[ASN][1000 genomes]
rs12428751	0.81[CHD][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.81[ASN][1000 genomes]
rs17073661	0.81[ASN][1000 genomes]
rs17073703	0.82[ASW][hapmap]
rs17660515	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2277452	1.00[ASW][hapmap];1.00[CEU][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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2482087	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2482089	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2482090	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2482091	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2482092	1.00[JPT][hapmap];0.97[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2482093	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2490264	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490265	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2490266	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490267	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2776952	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2776953	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2776955	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2776956	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2776958	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2776960	1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2776978	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2776979	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2776980	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2776981	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2776984	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2776985	1.00[CEU][hapmap];0.93[YRI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2776986	1.00[CEU][hapmap];0.93[YRI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2802240	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2802243	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2802244	0.84[ASW][hapmap];1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2802245	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2802246	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2802250	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2989592	1.00[CEU][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]
rs2989593	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2989596	1.00[ASN][1000 genomes]
rs3011619	0.89[MKK][hapmap]
rs3011620	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3011622	1.00[EUR][1000 genomes]
rs3011623	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3011624	1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3011625	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3013641	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs598281	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv983696	chr13:30034016-30090454	Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv430551	chr13:30061100-30113000	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv899960	chr13:30064014-30097240	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv561392	chr13:30071245-30091819	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30062400-30087200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr13:30071000-30128800	Strong transcription	Dnd41	blood
3	chr13:30077800-30087800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr13:30079600-30087200	Weak transcription	HUVEC	blood vessel
5	chr13:30080000-30087200	Weak transcription	Aorta	Aorta
6	chr13:30080200-30087200	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr13:30080200-30087800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr13:30080600-30088200	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr13:30081400-30087000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr13:30082000-30090200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr13:30082000-30106600	Weak transcription	Fetal Kidney	kidney
12	chr13:30082000-30107600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr13:30082200-30087000	Weak transcription	GM12878-XiMat	blood
14	chr13:30082200-30087400	Weak transcription	Primary B cells from peripheral blood	blood
15	chr13:30082200-30089800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr13:30082400-30087000	Weak transcription	Lung	lung
17	chr13:30082400-30087200	Weak transcription	NHLF	lung
18	chr13:30082800-30088800	Weak transcription	Hela-S3	cervix
19	chr13:30082800-30090000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr13:30082800-30096000	Weak transcription	Liver	Liver
21	chr13:30082800-30111600	Weak transcription	Stomach Mucosa	stomach
22	chr13:30083000-30087600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr13:30083200-30087600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr13:30083200-30087600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr13:30083200-30088400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr13:30083200-30089400	Weak transcription	Adipose Nuclei	Adipose
27	chr13:30083200-30107200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr13:30083400-30087400	Weak transcription	Right Ventricle	heart
29	chr13:30083400-30087600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr13:30083400-30089800	Weak transcription	Left Ventricle	heart
31	chr13:30083600-30094400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr13:30083600-30096400	Weak transcription	Small Intestine	intestine
33	chr13:30083800-30087600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr13:30084000-30087600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr13:30084000-30087800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr13:30084200-30087600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr13:30084200-30091200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr13:30084200-30091800	Strong transcription	Placenta Amnion	Placenta Amnion
39	chr13:30084200-30094800	Strong transcription	Thymus	Thymus
40	chr13:30084200-30106000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr13:30084200-30107800	Strong transcription	Esophagus	oesophagus
42	chr13:30084200-30110400	Strong transcription	Fetal Intestine Small	intestine
43	chr13:30084200-30110600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr13:30084200-30112600	Strong transcription	NHEK	skin
45	chr13:30084200-30115800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr13:30084400-30088200	Genic enhancers	Osteobl	bone
47	chr13:30084400-30111200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr13:30084600-30087800	Weak transcription	Fetal Heart	heart
49	chr13:30084600-30098000	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr13:30084600-30112200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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