Variant report

Variant	rs1737069
Chromosome Location	chr6:29730730-29730731
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:29725320..29727210-chr6:29727863..29730824,2	K562	blood:
2	chr6:29719431..29722230-chr6:29728984..29731849,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272236	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1476573	0.80[ASN][1000 genomes]
rs1610584	0.80[ASN][1000 genomes]
rs1610585	0.81[ASN][1000 genomes]
rs1610586	0.80[ASN][1000 genomes]
rs1610587	0.80[ASN][1000 genomes]
rs1610590	0.80[ASN][1000 genomes]
rs1610592	0.80[ASN][1000 genomes]
rs1610593	0.80[ASN][1000 genomes]
rs1610594	0.80[ASN][1000 genomes]
rs1610595	0.80[ASN][1000 genomes]
rs1610745	0.80[ASN][1000 genomes]
rs1611356	0.80[ASN][1000 genomes]
rs1611357	0.80[ASN][1000 genomes]
rs1611363	0.80[ASN][1000 genomes]
rs1611365	0.80[ASN][1000 genomes]
rs1611366	0.80[ASN][1000 genomes]
rs1611368	0.81[ASN][1000 genomes]
rs1611369	0.80[ASN][1000 genomes]
rs1611370	0.80[ASN][1000 genomes]
rs1611372	0.80[ASN][1000 genomes]
rs1611375	0.80[ASN][1000 genomes]
rs1611376	0.80[ASN][1000 genomes]
rs1611377	0.80[ASN][1000 genomes]
rs1611378	0.80[ASN][1000 genomes]
rs1611379	0.80[ASN][1000 genomes]
rs1627465	0.81[ASN][1000 genomes]
rs1633066	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1736913	0.91[ASN][1000 genomes]
rs1736919	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1736930	0.80[ASN][1000 genomes]
rs2072894	0.86[ASN][1000 genomes]
rs2076174	0.86[ASN][1000 genomes]
rs3116789	0.80[ASN][1000 genomes]
rs3116790	0.80[ASN][1000 genomes]
rs3131863	0.80[ASN][1000 genomes]
rs3823318	0.88[ASN][1000 genomes]
rs6901686	0.86[ASN][1000 genomes]
rs7751815	0.81[ASN][1000 genomes]
rs9258205	0.81[ASN][1000 genomes]
rs9258207	0.81[ASN][1000 genomes]
rs9258211	0.81[ASN][1000 genomes]
rs9258212	0.81[ASN][1000 genomes]
rs9258214	0.81[ASN][1000 genomes]
rs9258215	0.81[ASN][1000 genomes]
rs9258216	0.81[ASN][1000 genomes]
rs9258218	0.81[ASN][1000 genomes]
rs9258223	0.81[ASN][1000 genomes]
rs9258224	0.86[ASN][1000 genomes]
rs9258225	0.86[ASN][1000 genomes]
rs9258226	0.81[ASN][1000 genomes]
rs9258227	0.81[ASN][1000 genomes]
rs9258230	0.86[ASN][1000 genomes]
rs9258236	0.86[ASN][1000 genomes]
rs9258241	0.84[ASN][1000 genomes]
rs9258242	0.86[ASN][1000 genomes]
rs9258244	0.88[ASN][1000 genomes]
rs9258258	0.88[ASN][1000 genomes]
rs9258259	0.88[ASN][1000 genomes]
rs9258260	0.88[ASN][1000 genomes]
rs9258262	0.88[ASN][1000 genomes]
rs9258265	0.88[ASN][1000 genomes]
rs9258272	0.86[ASN][1000 genomes]
rs9258274	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv20940	chr6:29653954-29923410	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv428475	chr6:29659525-29763392	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv428139	chr6:29659525-29892317	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv427749	chr6:29659525-29975144	Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv508397	chr6:29663132-29761448	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	esv1794141	chr6:29670915-29765814	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv10809	chr6:29692573-29794119	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv883532	chr6:29703262-29814963	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	esv3441842	chr6:29715749-29942950	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
10	nsv883535	chr6:29725321-29741338	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
11	esv11180	chr6:29729381-29800066	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs1737069	HIST1H2BB	cis	cerebellum	SCAN
rs1737069	HCG4	cis	multi-tissue	Pritchard
rs1737069	HLA-F	cis	multi-tissue	Pritchard
rs1737069	FLJ35429	cis	multi-tissue	Pritchard
rs1737069	KIT	trans	multi-tissue	Pritchard
rs1737069	HLA-H	cis	multi-tissue	Pritchard
rs1737069	HLA-H	cis	lymphoblastoid	seeQTL
rs1737069	HLA-A	cis	multi-tissue	Pritchard
rs1737069	BTN2A1	cis	cerebellum	SCAN
rs1737069	ZKSCAN3	cis	cerebellum	SCAN
rs1737069	ZKSCAN3	cis	parietal	SCAN
rs1737069	NDUFS1	trans	multi-tissue	Pritchard

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29728400-29730800	Weak transcription	Spleen	Spleen
2	chr6:29728600-29737200	Weak transcription	Lung	lung
3	chr6:29728800-29731200	Weak transcription	Osteobl	bone
4	chr6:29729000-29733800	Enhancers	HMEC	breast
5	chr6:29729400-29733400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:29729600-29733200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:29729600-29733400	Enhancers	NHEK	skin
8	chr6:29729600-29733600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:29729600-29733600	Enhancers	Esophagus	oesophagus
10	chr6:29729800-29733800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:29730000-29732000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:29730200-29731000	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr6:29730200-29731000	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr6:29730200-29731200	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr6:29730200-29731600	Flanking Active TSS	Hela-S3	cervix
16	chr6:29730200-29731800	Enhancers	Adipose Nuclei	Adipose
17	chr6:29730200-29733000	Enhancers	HUVEC	blood vessel
18	chr6:29730200-29733400	Enhancers	NHDF-Ad	bronchial
19	chr6:29730200-29734600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:29730400-29730800	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr6:29730400-29730800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:29730400-29730800	Enhancers	Placenta Amnion	Placenta Amnion
23	chr6:29730400-29731200	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr6:29730400-29731200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:29730400-29731400	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr6:29730400-29732600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr6:29730400-29732800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr6:29730400-29733200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr6:29730600-29730800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
30	chr6:29730600-29731600	Enhancers	H1 Cell Line	embryonic stem cell
31	chr6:29730600-29731600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr6:29730600-29731800	Enhancers	Fetal Lung	lung
33	chr6:29730600-29732600	Enhancers	GM12878-XiMat	blood
34	chr6:29730600-29733400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr6:29730600-29733400	Enhancers	Muscle Satellite Cultured Cells	--

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