Variant report

Variant	rs556493
Chromosome Location	chr6:147549297-147549298
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:147221788..147226460-chr6:147542201..147549451,7	K562	blood:
2	chr6:147541756..147544397-chr6:147547163..147549434,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1039083	0.84[ASN][1000 genomes]
rs1039084	0.85[EUR][1000 genomes]
rs1039085	0.84[ASN][1000 genomes]
rs1039086	0.84[EUR][1000 genomes]
rs1147845	0.86[ASN][1000 genomes]
rs1147846	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1147847	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12173905	0.80[ASN][1000 genomes]
rs1221638	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12527235	0.85[EUR][1000 genomes]
rs1992389	0.85[EUR][1000 genomes]
rs2068111	0.87[ASN][1000 genomes]
rs2502732	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2582924	0.82[EUR][1000 genomes]
rs2582925	0.87[ASN][1000 genomes]
rs2582929	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2786183	0.85[EUR][1000 genomes]
rs2786185	0.86[EUR][1000 genomes]
rs2786187	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2786189	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2850177	0.86[ASN][1000 genomes]
rs486867	0.89[ASN][1000 genomes]
rs4896904	0.83[ASN][1000 genomes]
rs519630	0.92[EUR][1000 genomes]
rs562417	0.84[EUR][1000 genomes]
rs566028	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs577877	0.88[ASN][1000 genomes]
rs580657	0.88[EUR][1000 genomes]
rs584456	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs588273	0.84[ASN][1000 genomes]
rs591355	0.87[EUR][1000 genomes]
rs597631	0.87[EUR][1000 genomes]
rs598038	0.88[ASN][1000 genomes]
rs614476	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs617975	0.88[ASN][1000 genomes]
rs618474	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs619626	0.88[EUR][1000 genomes]
rs620715	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62435615	0.80[ASN][1000 genomes]
rs62435630	0.85[EUR][1000 genomes]
rs633603	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs657155	0.93[EUR][1000 genomes]
rs659399	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs664203	0.88[ASN][1000 genomes]
rs673944	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6928919	0.86[EUR][1000 genomes]
rs6932613	0.84[EUR][1000 genomes]
rs7762087	0.85[EUR][1000 genomes]
rs9373522	0.80[EUR][1000 genomes]
rs9377048	0.85[EUR][1000 genomes]
rs9399598	0.82[ASN][1000 genomes]
rs9497725	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

Variant related diseases (count:1)

Disease	PMID	Source
Bronchopulmonary dysplasia	23897914	GWAS catalog

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:147526000-147572200	Weak transcription	Lung	lung
2	chr6:147527200-147557800	Weak transcription	Fetal Stomach	stomach
3	chr6:147527200-147570000	Weak transcription	Left Ventricle	heart
4	chr6:147527200-147572000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:147527200-147572200	Weak transcription	Esophagus	oesophagus
6	chr6:147527400-147558800	Weak transcription	Primary B cells from cord blood	blood
7	chr6:147527400-147563800	Weak transcription	NH-A	brain
8	chr6:147527400-147566800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr6:147527400-147576400	Weak transcription	HSMMtube	muscle
10	chr6:147527600-147559600	Weak transcription	Colon Smooth Muscle	Colon
11	chr6:147527800-147586800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr6:147528200-147551800	Weak transcription	HUVEC	blood vessel
13	chr6:147528800-147565800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr6:147528800-147572000	Weak transcription	A549	lung
15	chr6:147529000-147572200	Weak transcription	Aorta	Aorta
16	chr6:147529400-147571800	Weak transcription	Fetal Brain Male	brain
17	chr6:147530000-147572000	Weak transcription	NHEK	skin
18	chr6:147533200-147572200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr6:147534000-147550800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:147534000-147572200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr6:147535800-147557600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:147537600-147572200	Weak transcription	Ovary	ovary
23	chr6:147537800-147571600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr6:147538200-147572200	Weak transcription	Spleen	Spleen
25	chr6:147538400-147572200	Weak transcription	Fetal Lung	lung
26	chr6:147538800-147572200	Weak transcription	Placenta	Placenta
27	chr6:147540200-147559200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr6:147540200-147569600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr6:147540200-147572000	Weak transcription	Thymus	Thymus
30	chr6:147540800-147561800	Weak transcription	Fetal Kidney	kidney
31	chr6:147542400-147590800	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr6:147542600-147549600	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr6:147543800-147552000	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr6:147543800-147556400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr6:147543800-147556800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr6:147543800-147556800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr6:147543800-147557600	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr6:147543800-147557800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr6:147543800-147557800	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr6:147543800-147559000	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr6:147543800-147560600	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr6:147543800-147561800	Weak transcription	Adipose Nuclei	Adipose
43	chr6:147543800-147562000	Weak transcription	NHLF	lung
44	chr6:147543800-147562600	Weak transcription	Brain Hippocampus Middle	brain
45	chr6:147543800-147563600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr6:147543800-147566200	Weak transcription	Stomach Mucosa	stomach
47	chr6:147543800-147572200	Weak transcription	Rectal Smooth Muscle	rectum
48	chr6:147543800-147588800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr6:147544000-147549400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr6:147544000-147553000	Weak transcription	Brain Anterior Caudate	brain

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