Variant report

Variant	rs7562299
Chromosome Location	chr2:189903415-189903416
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10178611	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10178886	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10181597	0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10194618	0.82[CHB][hapmap]
rs10194682	0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11686253	0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11690723	0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12622083	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12693526	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12693527	0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12693528	0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12989558	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13008197	0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13391332	0.96[YRI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13401377	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28486035	0.94[AFR][1000 genomes]
rs28758810	0.84[AFR][1000 genomes]
rs3923384	0.91[CHB][hapmap]
rs4666770	0.91[CHB][hapmap]
rs4667259	0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6414121	0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6434310	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6434311	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6434315	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6434316	0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6434317	0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6434318	0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6434321	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6434323	0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6738371	0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6760780	0.85[AFR][1000 genomes]
rs7420511	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7420715	0.91[CHB][hapmap]
rs7421040	0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7421525	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7423808	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7423973	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7424137	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7424790	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7426169	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7557945	0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7568732	0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7591905	0.91[AFR][1000 genomes]
rs7602447	0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7606293	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875610	chr2:189796272-189904674	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189888000-189917400	Weak transcription	Ovary	ovary
2	chr2:189889800-189931000	Weak transcription	Esophagus	oesophagus
3	chr2:189891600-189913600	Weak transcription	Fetal Kidney	kidney
4	chr2:189892000-189904000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:189893200-189932600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:189893600-189916200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr2:189894000-189913800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr2:189894600-189903800	Weak transcription	Placenta	Placenta
9	chr2:189894600-189932800	Weak transcription	Right Ventricle	heart
10	chr2:189895200-189909000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:189895200-189940800	Strong transcription	HSMM	muscle
12	chr2:189895600-189965200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:189896000-189907400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr2:189896200-189962400	Weak transcription	Left Ventricle	heart
15	chr2:189896400-189922600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:189896600-189910600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:189896800-189932800	Weak transcription	Pancreas	Pancrea
18	chr2:189897000-189911000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr2:189897000-189949000	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr2:189897200-189903600	Weak transcription	Fetal Intestine Small	intestine
21	chr2:189897200-189934400	Weak transcription	Gastric	stomach
22	chr2:189897400-189905800	Weak transcription	Brain Anterior Caudate	brain
23	chr2:189897400-189917400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr2:189897400-189932400	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr2:189897600-189934000	Weak transcription	Lung	lung
26	chr2:189898400-189938200	Weak transcription	HMEC	breast
27	chr2:189899000-189904000	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:189899000-189905000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr2:189899000-189916000	Weak transcription	Aorta	Aorta
30	chr2:189899000-189919000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:189899000-189925000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr2:189899000-189939200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:189899800-189903600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr2:189900000-189904000	Weak transcription	Colon Smooth Muscle	Colon
35	chr2:189900800-189964400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr2:189901000-189914200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr2:189901000-189919000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr2:189901200-189947400	Weak transcription	Fetal Brain Male	brain
39	chr2:189901400-189909000	Strong transcription	HSMMtube	muscle
40	chr2:189901600-189904000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr2:189901600-189907200	Strong transcription	Adipose Nuclei	Adipose
42	chr2:189901600-189908000	Strong transcription	Fetal Muscle Trunk	muscle
43	chr2:189901600-189911000	Strong transcription	A549	lung
44	chr2:189902000-189910600	Strong transcription	Stomach Smooth Muscle	stomach
45	chr2:189902200-189903800	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr2:189902200-189904400	Weak transcription	Primary T cells from cord blood	blood
47	chr2:189902400-189921600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr2:189902600-189906400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr2:189902600-189911200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:189902600-189914600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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