Variant report

Variant	rs2490264
Chromosome Location	chr13:30084535-30084536
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:30083698..30085805-chr13:30160713..30163555,2	MCF-7	breast:
2	chr13:30082618..30084607-chr13:30095133..30096907,2	K562	blood:

Variant related genes	Relation type
ENSG00000139514	Chromatin interaction

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[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]
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];0.95[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];0.95[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];0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2482093	1.00[JPT][hapmap];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];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2776952	0.85[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];0.95[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];0.95[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];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2776958	0.85[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];0.95[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];0.90[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];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2776980	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2776981	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2776984	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2776985	1.00[CEU][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2776986	1.00[CEU][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];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];0.95[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];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2802245	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2802246	0.82[AFR][1000 genomes];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];0.97[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	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3011622	0.80[AFR][1000 genomes];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]
rs3013640	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]
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:112 , 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	chr13:30074800-30084800	Weak transcription	Gastric	stomach
4	chr13:30077800-30085200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr13:30077800-30085600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr13:30077800-30087800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr13:30078000-30084800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr13:30078000-30086000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr13:30079000-30085800	Weak transcription	Primary T cells from cord blood	blood
10	chr13:30079600-30087200	Weak transcription	HUVEC	blood vessel
11	chr13:30080000-30084800	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr13:30080000-30085000	Weak transcription	HMEC	breast
13	chr13:30080000-30085600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr13:30080000-30087200	Weak transcription	Aorta	Aorta
15	chr13:30080200-30087200	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr13:30080200-30087800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr13:30080400-30085600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr13:30080400-30086600	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr13:30080600-30085000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr13:30080600-30086600	Weak transcription	Fetal Thymus	thymus
21	chr13:30080600-30088200	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr13:30081000-30084600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr13:30081000-30084600	Enhancers	Fetal Heart	heart
24	chr13:30081200-30085000	Weak transcription	Primary hematopoietic stem cells	blood
25	chr13:30081200-30085600	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr13:30081400-30086800	Weak transcription	A549	lung
27	chr13:30081400-30087000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr13:30081800-30085400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr13:30081800-30086000	Enhancers	Fetal Brain Male	brain
30	chr13:30081800-30086200	Enhancers	Fetal Muscle Leg	muscle
31	chr13:30081800-30086400	Enhancers	NHDF-Ad	bronchial
32	chr13:30082000-30084800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr13:30082000-30084800	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr13:30082000-30090200	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr13:30082000-30106600	Weak transcription	Fetal Kidney	kidney
36	chr13:30082000-30107600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr13:30082200-30084600	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr13:30082200-30085000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr13:30082200-30087000	Weak transcription	GM12878-XiMat	blood
40	chr13:30082200-30087400	Weak transcription	Primary B cells from peripheral blood	blood
41	chr13:30082200-30089800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr13:30082400-30085000	Enhancers	Fetal Muscle Trunk	muscle
43	chr13:30082400-30085600	Weak transcription	Ovary	ovary
44	chr13:30082400-30085800	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr13:30082400-30087000	Weak transcription	Lung	lung
46	chr13:30082400-30087200	Weak transcription	NHLF	lung
47	chr13:30082600-30084600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr13:30082600-30084800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr13:30082600-30086800	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr13:30082800-30084600	Weak transcription	Brain Cingulate Gyrus	brain

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