Variant report

Variant	rs4942809
Chromosome Location	chr13:49833774-49833775
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10459375	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10459376	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11843587	0.82[EUR][1000 genomes]
rs12385878	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12585196	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1924659	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1924660	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1924661	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2038759	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2147398	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2181905	0.86[EUR][1000 genomes]
rs2274149	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2274150	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2407521	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2407607	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2407608	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2407609	0.88[ASN][1000 genomes]
rs3087770	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3764131	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4245351	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4941637	0.82[EUR][1000 genomes]
rs4942811	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942812	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4942815	0.82[EUR][1000 genomes]
rs6561511	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs719614	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7320595	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7320745	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326181	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7326191	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7328063	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7330892	0.81[EUR][1000 genomes]
rs7334929	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7984689	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7988621	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7997545	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7999710	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9316434	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316437	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9316439	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9526533	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526534	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526535	0.86[ASN][1000 genomes]
rs9526537	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9526538	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9526539	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535173	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535174	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535177	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535180	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535181	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535182	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535184	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535185	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535190	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535192	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535193	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535194	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535197	0.84[EUR][1000 genomes]
rs9535198	0.82[EUR][1000 genomes]
rs9535199	0.81[EUR][1000 genomes]
rs9562873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568174	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9568176	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9568177	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9568179	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9568181	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9568182	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9591249	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9596077	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9596078	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9596079	0.81[EUR][1000 genomes]
rs9596080	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv832607	chr13:49756458-49920894	Flanking Bivalent TSS/Enh Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv900069	chr13:49815405-49976393	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49823000-49833800	Weak transcription	Brain Cingulate Gyrus	brain
2	chr13:49823000-49833800	Weak transcription	Fetal Brain Male	brain
3	chr13:49823000-49836400	Weak transcription	Colonic Mucosa	Colon
4	chr13:49823000-49837000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr13:49823000-49838000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr13:49823000-49838200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr13:49823000-49844200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr13:49823400-49835000	Weak transcription	Hela-S3	cervix
9	chr13:49823400-49837200	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr13:49823400-49837400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr13:49823400-49837600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr13:49823400-49844000	Weak transcription	A549	lung
13	chr13:49823600-49833800	Weak transcription	Colon Smooth Muscle	Colon
14	chr13:49823600-49835200	Weak transcription	K562	blood
15	chr13:49823600-49837400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr13:49823600-49843200	Weak transcription	NHEK	skin
17	chr13:49823800-49855400	Weak transcription	Small Intestine	intestine
18	chr13:49824000-49834600	Weak transcription	Fetal Heart	heart
19	chr13:49826400-49833800	Weak transcription	Spleen	Spleen
20	chr13:49826600-49877800	Weak transcription	Psoas Muscle	Psoas
21	chr13:49827600-49837200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr13:49827800-49834800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr13:49827800-49837000	Strong transcription	Fetal Muscle Trunk	muscle
24	chr13:49827800-49837800	Strong transcription	Fetal Lung	lung
25	chr13:49827800-49839400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr13:49828800-49836600	Strong transcription	Fetal Muscle Leg	muscle
27	chr13:49828800-49837200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr13:49829200-49835400	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr13:49829200-49836000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr13:49830400-49835200	Strong transcription	HepG2	liver
31	chr13:49830600-49834200	Weak transcription	Right Ventricle	heart
32	chr13:49831200-49837600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr13:49831200-49845200	Weak transcription	NH-A	brain
34	chr13:49831400-49834400	Weak transcription	HUVEC	blood vessel
35	chr13:49831600-49837000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr13:49831600-49837000	Strong transcription	Fetal Stomach	stomach
37	chr13:49831800-49836200	Strong transcription	Fetal Brain Female	brain
38	chr13:49832000-49843000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr13:49832200-49836200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr13:49832400-49837000	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr13:49832600-49833800	Weak transcription	Duodenum Mucosa	Duodenum
42	chr13:49832600-49833800	Weak transcription	Left Ventricle	heart
43	chr13:49832600-49833800	Weak transcription	NHLF	lung
44	chr13:49832600-49836400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr13:49832600-49836400	Strong transcription	Fetal Thymus	thymus
46	chr13:49832600-49836600	Strong transcription	Primary B cells from cord blood	blood
47	chr13:49832800-49833800	Weak transcription	HSMM	muscle
48	chr13:49832800-49834000	Weak transcription	GM12878-XiMat	blood
49	chr13:49832800-49835600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr13:49832800-49836600	Strong transcription	Stomach Smooth Muscle	stomach

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