Variant report

Variant	rs2200224
Chromosome Location	chr4:53738516-53738517
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10517269	0.90[YRI][hapmap]
rs1109696	0.91[ASW][hapmap];0.89[YRI][hapmap]
rs11932601	0.84[ASW][hapmap];0.89[YRI][hapmap]
rs11938159	0.94[YRI][hapmap]
rs11939448	0.88[YRI][hapmap]
rs17082084	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes]
rs2007936	0.89[YRI][hapmap]
rs2007959	0.90[ASW][hapmap];0.89[YRI][hapmap]
rs56211634	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6554057	0.84[YRI][hapmap]
rs6817433	0.89[YRI][hapmap]
rs6818178	1.00[YRI][hapmap]
rs6824279	0.90[AMR][1000 genomes]
rs6838718	0.84[ASW][hapmap];1.00[YRI][hapmap]
rs6847299	0.91[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs6858566	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap]
rs73814893	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73814894	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73814895	1.00[EUR][1000 genomes]
rs755523	1.00[AMR][1000 genomes]
rs7655781	0.88[YRI][hapmap]
rs7681701	0.90[AMR][1000 genomes]
rs7681744	0.90[AMR][1000 genomes]
rs7688141	0.84[YRI][hapmap]
rs7699960	0.85[YRI][hapmap]
rs881744	1.00[YRI][hapmap]

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	nsv1004889	chr4:53436500-54106281	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv537094	chr4:53436500-54106281	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1004086	chr4:53698581-53773183	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:53729200-53751200	Weak transcription	GM12878-XiMat	blood
2	chr4:53729200-53807800	Weak transcription	Esophagus	oesophagus
3	chr4:53729400-53738600	Weak transcription	HMEC	breast
4	chr4:53729400-53739200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:53729400-53743200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr4:53729400-53752400	Weak transcription	Primary B cells from cord blood	blood
7	chr4:53729400-53753800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr4:53729600-53739400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:53729600-53739600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr4:53729600-53742200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr4:53729800-53739400	Weak transcription	Fetal Intestine Large	intestine
12	chr4:53730000-53743800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr4:53731400-53751000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr4:53731600-53739400	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr4:53732400-53750200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr4:53732400-53755000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr4:53732800-53739400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr4:53732800-53749400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr4:53733000-53767800	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr4:53733200-53759000	Weak transcription	Osteobl	bone
21	chr4:53733400-53739200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr4:53733600-53740400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr4:53733600-53750200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:53733800-53739200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr4:53734000-53738800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr4:53734000-53739600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr4:53734000-53749200	Weak transcription	Aorta	Aorta
28	chr4:53734200-53742200	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr4:53734200-53760800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr4:53734600-53739000	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr4:53734600-53739400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr4:53734600-53822400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr4:53734800-53739000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr4:53735000-53740200	Weak transcription	Fetal Kidney	kidney
35	chr4:53735000-53770200	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr4:53735200-53755200	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr4:53735200-53778000	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr4:53735400-53742000	Weak transcription	Dnd41	blood
39	chr4:53735600-53739400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr4:53735600-53740400	Weak transcription	Lung	lung
41	chr4:53735600-53751600	Weak transcription	Spleen	Spleen
42	chr4:53735800-53739000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr4:53735800-53739400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr4:53735800-53740000	Weak transcription	Pancreas	Pancrea
45	chr4:53735800-53772600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr4:53736000-53739200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr4:53736000-53739400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr4:53736000-53740400	Weak transcription	Right Ventricle	heart
49	chr4:53736000-53750600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr4:53736000-53752600	Weak transcription	Primary hematopoietic stem cells	blood

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