Variant report

Variant	rs7699960
Chromosome Location	chr4:53735661-53735662
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:53726210..53731066-chr4:53734664..53738356,6	MCF-7	breast:
2	chr4:53735307..53737549-chr4:53739100..53741985,3	K562	blood:
3	chr4:53734594..53736785-chr4:53744085..53747045,2	K562	blood:

Variant related genes	Relation type
ENSG00000128045	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10517269	0.85[CHB][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.82[AMR][1000 genomes]
rs11932601	0.85[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11938159	0.82[CHB][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes]
rs11939448	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs17082084	0.85[YRI][hapmap]
rs2200225	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3811781	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41279517	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58577680	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6554054	0.80[AMR][1000 genomes]
rs6554057	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6817433	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6818178	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6833350	0.81[EUR][1000 genomes]
rs6838718	0.85[ASW][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.85[YRI][hapmap];0.80[AMR][1000 genomes]
rs6848200	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6855240	0.81[EUR][1000 genomes]
rs6858566	0.90[YRI][hapmap]
rs73814868	0.82[AMR][1000 genomes]
rs73814875	0.87[ASN][1000 genomes]
rs73814883	0.92[ASN][1000 genomes]
rs73814886	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7655781	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7670068	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7677726	0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs7685816	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7688141	0.82[JPT][hapmap];0.80[AMR][1000 genomes]
rs881744	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.82[MEX][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][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	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	chr4:53728800-53738400	Weak transcription	Small Intestine	intestine
2	chr4:53729200-53751200	Weak transcription	GM12878-XiMat	blood
3	chr4:53729200-53807800	Weak transcription	Esophagus	oesophagus
4	chr4:53729400-53738600	Weak transcription	HMEC	breast
5	chr4:53729400-53739200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:53729400-53743200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr4:53729400-53752400	Weak transcription	Primary B cells from cord blood	blood
8	chr4:53729400-53753800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr4:53729600-53739400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:53729600-53739600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr4:53729600-53742200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr4:53729800-53737000	Weak transcription	Primary T cells from cord blood	blood
13	chr4:53729800-53739400	Weak transcription	Fetal Intestine Large	intestine
14	chr4:53730000-53743800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr4:53730200-53736600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:53731200-53736000	Enhancers	Right Atrium	heart
17	chr4:53731400-53751000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr4:53731600-53736200	Weak transcription	Stomach Mucosa	stomach
19	chr4:53731600-53739400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr4:53731800-53736600	Weak transcription	Colon Smooth Muscle	Colon
21	chr4:53731800-53738000	Weak transcription	Liver	Liver
22	chr4:53732400-53750200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr4:53732400-53755000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr4:53732800-53737400	Weak transcription	Fetal Intestine Small	intestine
25	chr4:53732800-53738400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr4:53732800-53739400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr4:53732800-53749400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr4:53733000-53736000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr4:53733000-53767800	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr4:53733200-53737600	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr4:53733200-53759000	Weak transcription	Osteobl	bone
32	chr4:53733400-53737200	Enhancers	Fetal Heart	heart
33	chr4:53733400-53739200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr4:53733600-53736800	Enhancers	Brain Germinal Matrix	brain
35	chr4:53733600-53737200	Enhancers	Fetal Muscle Leg	muscle
36	chr4:53733600-53740400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr4:53733600-53750200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr4:53733800-53736000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr4:53733800-53736000	Enhancers	Right Ventricle	heart
40	chr4:53733800-53737200	Enhancers	Fetal Lung	lung
41	chr4:53733800-53737200	Enhancers	Left Ventricle	heart
42	chr4:53733800-53739200	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr4:53734000-53735800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr4:53734000-53736000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr4:53734000-53736400	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr4:53734000-53736400	Enhancers	Fetal Brain Male	brain
47	chr4:53734000-53736600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr4:53734000-53736800	Enhancers	Brain Angular Gyrus	brain
49	chr4:53734000-53738800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr4:53734000-53739600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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