Variant report

Variant	rs6639
Chromosome Location	chr5:179156782-179156783
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SP1	chr5:179156177-179156796	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr5:179156244-179156839	HL-60	blood:	n/a	n/a
3	POLR2A	chr5:179153683-179159964	K562	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:177630086..177632687-chr5:179156675..179158833,2	K562	blood:
2	chr5:179125428..179127491-chr5:179155880..179157495,2	K562	blood:
3	chr5:179152255..179157364-chr5:179157617..179161141,8	K562	blood:
4	chr5:179122873..179128898-chr5:179155888..179164921,20	K562	blood:
5	chr5:179147273..179149282-chr5:179155008..179157587,2	MCF-7	breast:
6	chr5:179148343..179151345-chr5:179156498..179159040,4	K562	blood:
7	chr5:179129274..179131035-chr5:179155362..179157938,2	K562	blood:
8	chr5:179143486..179153989-chr5:179156108..179164461,19	MCF-7	breast:
9	chr5:179154467..179157010-chr5:179247378..179249418,2	K562	blood:
10	chr5:179133916..179136013-chr5:179154782..179157168,2	K562	blood:

No data

Variant related genes	Relation type
MAML1	TF binding region
ENSG00000127022	Chromatin interaction
ENSG00000161021	Chromatin interaction
ENSG00000161011	Chromatin interaction
ENSG00000197451	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11738269	1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11738720	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11739042	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11740569	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11741570	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11743232	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11744616	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11746924	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11747496	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12522263	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1469020	1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs1469021	1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs17617068	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17617710	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34057110	0.81[AMR][1000 genomes]
rs3756614	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3797762	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3797776	1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs41458244	0.83[ASN][1000 genomes]
rs4700838	1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4700840	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4701196	0.83[ASN][1000 genomes]
rs55654737	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs55827522	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55975622	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56309143	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56335144	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58386410	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62404347	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62406176	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62406177	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62406178	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62406181	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62406187	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62406219	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62406223	0.81[ASN][1000 genomes]
rs6601067	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6601072	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6860716	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6887507	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6893300	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6895902	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs730012	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7444006	1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7447159	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7704520	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7705530	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7709723	1.00[ASW][hapmap];0.92[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.84[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7715356	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7734102	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7735702	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949554	chr5:178832325-179309513	Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
2	nsv883270	chr5:178951106-179350387	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	312 gene(s)	inside rSNPs	diseases
3	nsv830560	chr5:179039212-179175758	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
4	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6639	CANX	cis	parietal	SCAN
rs6639	CANX	cis	cerebellum	SCAN
rs6639	TRIM52	cis	parietal	SCAN
rs6639	C5orf45	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179127800-179158200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr5:179128400-179157800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr5:179128400-179157800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr5:179128400-179158200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr5:179128400-179159200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:179128600-179158200	Strong transcription	Fetal Muscle Leg	muscle
7	chr5:179129000-179158200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr5:179129200-179157600	Strong transcription	Fetal Muscle Trunk	muscle
9	chr5:179129400-179158200	Strong transcription	Fetal Thymus	thymus
10	chr5:179129600-179157400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr5:179129800-179158200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr5:179129800-179158200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr5:179129800-179158200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr5:179129800-179158200	Strong transcription	Fetal Intestine Large	intestine
15	chr5:179129800-179158800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr5:179130400-179158200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr5:179130600-179157000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr5:179130600-179157600	Strong transcription	HUVEC	blood vessel
19	chr5:179130800-179158200	Strong transcription	Primary B cells from peripheral blood	blood
20	chr5:179130800-179158200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr5:179130800-179159800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr5:179131000-179157600	Strong transcription	Muscle Satellite Cultured Cells	--
23	chr5:179131000-179157800	Strong transcription	Dnd41	blood
24	chr5:179131000-179158200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr5:179131200-179158000	Strong transcription	Placenta	Placenta
26	chr5:179132000-179158200	Strong transcription	Duodenum Mucosa	Duodenum
27	chr5:179132400-179157400	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr5:179132400-179157400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr5:179132800-179158200	Strong transcription	Adipose Nuclei	Adipose
30	chr5:179132800-179158200	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr5:179133000-179158000	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr5:179133000-179158200	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr5:179133000-179158200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr5:179133000-179158200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr5:179133000-179158200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr5:179133200-179158400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr5:179133200-179158600	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr5:179133200-179158800	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr5:179133400-179157000	Strong transcription	Stomach Smooth Muscle	stomach
40	chr5:179133600-179158200	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr5:179136600-179156800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
42	chr5:179138400-179159000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr5:179139400-179157600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
44	chr5:179139400-179157800	Strong transcription	Left Ventricle	heart
45	chr5:179139400-179158000	Strong transcription	H9 Cell Line	embryonic stem cell
46	chr5:179140000-179156800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr5:179140600-179158000	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr5:179142600-179157000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr5:179143000-179156800	Strong transcription	Fetal Lung	lung
50	chr5:179144400-179158200	Strong transcription	Primary T helper cells fromperipheralblood	blood

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