Variant report

Variant	rs6665473
Chromosome Location	chr1:153650008-153650009
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr1:153649799-153651422	SK-N-SH	brain:	n/a	chr1:153650334-153650353
2	CTCF	chr1:153649966-153652441	SK-N-SH	brain:	n/a	chr1:153650334-153650350 chr1:153650333-153650351 chr1:153650335-153650356
3	FOXM1	chr1:153649968-153650633	GM12878	blood:	n/a	n/a
4	RAD21	chr1:153649934-153650820	A549	lung:	n/a	chr1:153650334-153650353
5	CTCF	chr1:153649860-153650010	HL-60	blood:	n/a	n/a
6	RAD21	chr1:153649897-153650806	HCT-116	colon:	n/a	chr1:153650334-153650353
7	CTCF	chr1:153649940-153650090	A549	lung:	n/a	n/a
8	CTCF	chr1:153649982-153650756	HCT-116	colon:	n/a	chr1:153650334-153650350 chr1:153650333-153650351 chr1:153650335-153650356
9	SMC3	chr1:153649978-153652192	SK-N-SH	brain:	n/a	chr1:153650335-153650349
10	CTCF	chr1:153649825-153651230	A549	lung:	n/a	chr1:153650334-153650350 chr1:153650333-153650351 chr1:153650335-153650356
11	RAD21	chr1:153649970-153650848	ECC-1	luminal epithelium:	n/a	chr1:153650334-153650353
12	CTCF	chr1:153649918-153650770	HCT-116	colon:	n/a	chr1:153650334-153650350 chr1:153650333-153650351 chr1:153650335-153650356

No.	Distal block	Cell Line	Cell type
1	chr1:153648746..153650571-chr1:153732121..153733680,2	K562	blood:
2	chr1:153649895..153650654-chr1:153744097..153745019,3	MCF-7	breast:
3	chr1:153649935..153650729-chr1:153769678..153770330,2	MCF-7	breast:
4	chr1:153598471..153600111-chr1:153647680..153650652,2	K562	blood:
5	chr1:153643161..153645912-chr1:153648734..153650350,3	K562	blood:
6	chr1:153648500..153651688-chr1:153746725..153749419,3	MCF-7	breast:
7	chr1:153649938..153650840-chr1:153744033..153745088,8	K562	blood:
8	chr1:153649883..153650429-chr1:153918649..153919534,2	MCF-7	breast:
9	chr1:153649899..153650723-chr1:153958862..153959802,2	MCF-7	breast:
10	chr1:153544558..153545159-chr1:153649999..153650713,2	MCF-7	breast:
11	chr1:153648416..153650941-chr1:153651143..153653959,2	MCF-7	breast:
12	chr1:153649841..153650855-chr1:153721578..153722543,22	MCF-7	breast:
13	chr1:153649784..153650665-chr1:153769233..153770264,3	K562	blood:
14	chr1:153330243..153332456-chr1:153649473..153651392,2	K562	blood:
15	chr1:153649848..153650713-chr1:153958953..153960063,4	K562	blood:

Variant related genes	Relation type
NPR1	TF binding region
ENSG00000143621	Chromatin interaction
ENSG00000169418	Chromatin interaction
ENSG00000143624	Chromatin interaction
ENSG00000198837	Chromatin interaction
ENSG00000163220	Chromatin interaction
ENSG00000189171	Chromatin interaction
ENSG00000143554	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs16835525	1.00[ASW][hapmap]
rs35102232	1.00[EUR][1000 genomes]
rs6663046	1.00[ASN][1000 genomes]
rs7547692	1.00[EUR][1000 genomes]
rs9427340	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9427391	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv547928	chr1:153612133-153714252	Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	esv2830411	chr1:153613393-153725007	Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	nsv1067771	chr1:153613593-153724866	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
6	nsv530052	chr1:153613593-153724866	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	nsv1005818	chr1:153613597-153724980	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	nsv535173	chr1:153613597-153724980	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
9	nsv1007835	chr1:153613597-153729959	Genic enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
10	nsv535174	chr1:153613597-153729959	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
11	nsv1011897	chr1:153613597-153836703	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
12	nsv464028	chr1:153622220-153723037	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
13	nsv547929	chr1:153622220-153723037	Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
14	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
15	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
16	nsv1001312	chr1:153622834-153724867	Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
17	nsv535176	chr1:153622834-153724867	Active TSS Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6665473	MSX1	trans	lymphoblastoid	seeQTL

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153644600-153650400	Weak transcription	Esophagus	oesophagus
2	chr1:153645000-153650200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:153645000-153650200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:153648600-153650400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:153649800-153650200	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
6	chr1:153649800-153650400	Weak transcription	Left Ventricle	heart
7	chr1:153650000-153650200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
8	chr1:153650000-153650200	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr1:153650000-153650200	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr1:153650000-153650200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:153650000-153650200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:153650000-153650200	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:153650000-153650200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:153650000-153650200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:153650000-153650200	Enhancers	Adipose Nuclei	Adipose
16	chr1:153650000-153650200	Enhancers	Liver	Liver
17	chr1:153650000-153650200	Active TSS	Brain Cingulate Gyrus	brain
18	chr1:153650000-153650200	Bivalent Enhancer	Brain Germinal Matrix	brain
19	chr1:153650000-153650200	Bivalent/Poised TSS	Fetal Brain Male	brain
20	chr1:153650000-153650200	Bivalent Enhancer	Fetal Brain Female	brain
21	chr1:153650000-153650200	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr1:153650000-153650200	Bivalent Enhancer	Stomach Mucosa	stomach
23	chr1:153650000-153650400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:153650000-153650400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:153650000-153650400	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr1:153650000-153650400	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
27	chr1:153650000-153650400	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
28	chr1:153650000-153650400	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr1:153650000-153650400	Flanking Active TSS	Brain Angular Gyrus	brain
30	chr1:153650000-153650400	Bivalent Enhancer	Brain Hippocampus Middle	brain
31	chr1:153650000-153650400	Enhancers	Brain Substantia Nigra	brain
32	chr1:153650000-153650400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr1:153650000-153650400	Enhancers	Fetal Heart	heart
34	chr1:153650000-153650400	Enhancers	Pancreatic Islets	Pancreatic Islet
35	chr1:153650000-153650400	Bivalent Enhancer	Fetal Muscle Leg	muscle
36	chr1:153650000-153650400	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
37	chr1:153650000-153650400	Enhancers	HepG2	liver
38	chr1:153650000-153650400	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
39	chr1:153650000-153650600	Bivalent Enhancer	Primary T cells from cord blood	blood
40	chr1:153650000-153650600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
41	chr1:153650000-153650600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
42	chr1:153650000-153650600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
43	chr1:153650000-153650600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
44	chr1:153650000-153650600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:153650000-153650600	Bivalent Enhancer	Colon Smooth Muscle	Colon
46	chr1:153650000-153650600	Bivalent Enhancer	Fetal Stomach	stomach
47	chr1:153650000-153650800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
48	chr1:153650000-153650800	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
49	chr1:153650000-153650800	Flanking Active TSS	Hela-S3	cervix
50	chr1:153650000-153650800	Enhancers	K562	blood

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