Variant report

Variant	rs474990
Chromosome Location	chr6:147572380-147572381
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	chr6:147570692..147572642-chr6:147580577..147582832,2	MCF-7	breast:
2	chr6:147570173..147572962-chr6:147576488..147578515,2	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1039083	0.96[EUR][1000 genomes]
rs1039085	0.96[EUR][1000 genomes]
rs1147844	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1147845	0.93[EUR][1000 genomes]
rs1147847	0.80[EUR][1000 genomes]
rs1496033	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1496034	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1660687	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1992389	0.80[EUR][1000 genomes]
rs2047286	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2068111	0.96[EUR][1000 genomes]
rs2119490	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2218221	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2502732	0.82[EUR][1000 genomes]
rs2582925	0.98[EUR][1000 genomes]
rs2582929	0.80[EUR][1000 genomes]
rs2786183	0.80[EUR][1000 genomes]
rs2786184	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2786185	0.81[EUR][1000 genomes]
rs2850177	0.95[EUR][1000 genomes]
rs2850178	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs486867	0.98[EUR][1000 genomes]
rs4896904	0.95[EUR][1000 genomes]
rs4896905	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4896906	0.87[EUR][1000 genomes]
rs4896908	0.83[EUR][1000 genomes]
rs533201	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs577877	0.96[EUR][1000 genomes]
rs580657	0.82[EUR][1000 genomes]
rs588273	0.96[EUR][1000 genomes]
rs591355	0.82[EUR][1000 genomes]
rs597631	0.82[EUR][1000 genomes]
rs598038	0.96[EUR][1000 genomes]
rs608147	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs614476	0.81[EUR][1000 genomes]
rs617975	0.98[EUR][1000 genomes]
rs618474	0.82[EUR][1000 genomes]
rs619175	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs619626	0.82[EUR][1000 genomes]
rs620715	0.83[EUR][1000 genomes]
rs62435630	0.80[EUR][1000 genomes]
rs633603	0.82[EUR][1000 genomes]
rs657155	0.88[ASN][1000 genomes]
rs664203	0.98[EUR][1000 genomes]
rs7748995	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7762087	0.80[EUR][1000 genomes]
rs9373523	0.83[ASN][1000 genomes]
rs9377048	0.80[EUR][1000 genomes]
rs9390458	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9390462	0.83[ASN][1000 genomes]
rs9399598	0.95[EUR][1000 genomes]
rs9403852	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9497759	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs995697	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019245	chr6:147350834-147609776	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv538467	chr6:147350834-147609776	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv886752	chr6:147443480-147729477	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv886753	chr6:147526508-147680291	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv470864	chr6:147539165-147709179	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv886754	chr6:147539165-147729477	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv604840	chr6:147539165-147730324	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
8	esv1832155	chr6:147554900-147715464	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:147527400-147576400	Weak transcription	HSMMtube	muscle
2	chr6:147527800-147586800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr6:147542400-147590800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr6:147543800-147588800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr6:147544200-147574200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr6:147544400-147574800	Weak transcription	HepG2	liver
7	chr6:147545600-147617000	Weak transcription	Small Intestine	intestine
8	chr6:147549400-147616800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr6:147549600-147578200	Weak transcription	Fetal Heart	heart
10	chr6:147549600-147584600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr6:147549600-147587200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr6:147552600-147591800	Weak transcription	HUVEC	blood vessel
13	chr6:147554600-147590000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr6:147556200-147574600	Strong transcription	Muscle Satellite Cultured Cells	--
15	chr6:147560200-147574200	Weak transcription	Dnd41	blood
16	chr6:147561600-147600800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr6:147562600-147599800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr6:147564000-147586800	Weak transcription	HMEC	breast
19	chr6:147564400-147604600	Weak transcription	NHLF	lung
20	chr6:147564400-147619000	Weak transcription	Hela-S3	cervix
21	chr6:147564600-147608800	Weak transcription	NH-A	brain
22	chr6:147564600-147617000	Weak transcription	Fetal Kidney	kidney
23	chr6:147565600-147572600	Strong transcription	Osteobl	bone
24	chr6:147566200-147574000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr6:147566200-147574400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:147566400-147573400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr6:147566600-147574600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr6:147566800-147574200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr6:147569400-147573600	Strong transcription	Duodenum Mucosa	Duodenum
30	chr6:147569600-147573200	Strong transcription	Fetal Intestine Large	intestine
31	chr6:147569600-147574200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:147569800-147572400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:147569800-147573200	ZNF genes & repeats	K562	blood
34	chr6:147570000-147573000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr6:147570000-147573200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr6:147570000-147573200	Strong transcription	Left Ventricle	heart
37	chr6:147570000-147573200	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr6:147570200-147587200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr6:147570400-147572400	Weak transcription	Primary B cells from peripheral blood	blood
40	chr6:147570600-147573200	Weak transcription	Psoas Muscle	Psoas
41	chr6:147570600-147609000	Weak transcription	Brain Substantia Nigra	brain
42	chr6:147570800-147573800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr6:147571200-147574200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr6:147571200-147574600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr6:147571200-147574600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr6:147571400-147573200	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr6:147571400-147574600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr6:147571400-147574800	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr6:147571400-147599200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr6:147571400-147599400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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