Variant report

Variant	rs6861279
Chromosome Location	chr5:74919409-74919410
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:74913060..74915078-chr5:74915803..74919443,3	K562	blood:
2	chr5:74910178..74911723-chr5:74917267..74920194,2	K562	blood:
3	chr5:74912858..74914560-chr5:74917246..74919606,2	K562	blood:
4	chr5:74919304..74922816-chr5:74930966..74933826,3	K562	blood:

Variant related genes	Relation type
ENSG00000189045	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10038723	0.87[EUR][1000 genomes]
rs10043621	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10044053	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10060260	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10067641	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10075139	0.91[EUR][1000 genomes]
rs10434644	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10474436	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1051795	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10942739	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13354407	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1427924	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17739580	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1863934	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1863935	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1995267	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2287711	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs253392	0.81[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs253393	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs253407	0.95[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs253408	0.88[ASN][1000 genomes]
rs253409	0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2878519	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2878520	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213801	0.94[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34340	0.95[ASN][1000 genomes]
rs34344	0.87[ASN][1000 genomes]
rs34345	0.87[ASN][1000 genomes]
rs34350	0.82[ASN][1000 genomes]
rs4045166	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4385188	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4440336	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4703674	0.85[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4704224	0.82[EUR][1000 genomes]
rs4704228	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57149337	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57312935	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5744533	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5744555	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5744575	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5744595	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5744598	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5744601	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5744621	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5744663	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5744703	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59506842	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61430233	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67969809	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6863398	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6872314	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6874781	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6886841	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6891949	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73120833	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7445415	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs767676	0.85[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7706857	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7709282	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7717505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7723531	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs924452	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9293656	0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9332464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][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	nsv882194	chr5:74656175-74946455	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv882197	chr5:74692776-74946455	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv882199	chr5:74757758-74946455	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv1027368	chr5:74759999-75663712	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv882202	chr5:74808417-74946455	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv518475	chr5:74863041-75411804	Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	esv1850196	chr5:74890618-75138443	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6861279	GCNT4	cis	cerebellum	SCAN
rs6861279	HMGCR	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74907800-74921400	Weak transcription	Aorta	Aorta
2	chr5:74907800-74921400	Weak transcription	Lung	lung
3	chr5:74908200-74919600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr5:74908200-74923600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr5:74908600-74920400	Enhancers	Fetal Intestine Small	intestine
6	chr5:74913800-74919800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr5:74913800-74921400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr5:74913800-74921600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:74913800-74922400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr5:74913800-74922800	Weak transcription	Ovary	ovary
11	chr5:74913800-74923600	Weak transcription	Esophagus	oesophagus
12	chr5:74913800-74923600	Weak transcription	Fetal Muscle Leg	muscle
13	chr5:74913800-74933600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr5:74914000-74919800	Weak transcription	Fetal Stomach	stomach
15	chr5:74914000-74923400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr5:74914000-74930800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr5:74915000-74925800	Weak transcription	Fetal Muscle Trunk	muscle
18	chr5:74915600-74921800	Enhancers	Stomach Mucosa	stomach
19	chr5:74915800-74920000	Enhancers	Duodenum Mucosa	Duodenum
20	chr5:74916600-74931800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr5:74916800-74919600	Weak transcription	K562	blood
22	chr5:74917000-74919800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr5:74917000-74920000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr5:74917000-74923400	Weak transcription	Gastric	stomach
25	chr5:74917600-74920200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr5:74917800-74920000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr5:74917800-74920000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr5:74917800-74920200	Enhancers	HMEC	breast
29	chr5:74917800-74920400	Enhancers	Fetal Intestine Large	intestine
30	chr5:74918000-74920200	Enhancers	NHEK	skin
31	chr5:74918400-74919600	Weak transcription	Small Intestine	intestine
32	chr5:74918400-74944200	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr5:74918800-74919800	Weak transcription	HepG2	liver
34	chr5:74918800-74920000	Weak transcription	Liver	Liver
35	chr5:74918800-74934000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr5:74919400-74919600	Enhancers	HSMM	muscle
37	chr5:74919400-74920200	Enhancers	Muscle Satellite Cultured Cells	--
38	chr5:74919400-74920200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr5:74919400-74920200	Enhancers	Fetal Heart	heart
40	chr5:74919400-74920200	Enhancers	HSMMtube	muscle
41	chr5:74919400-74920200	Enhancers	NHDF-Ad	bronchial
42	chr5:74919400-74920400	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr5:74919400-74920400	Flanking Active TSS	A549	lung
44	chr5:74919400-74920600	Enhancers	Rectal Mucosa Donor 31	rectum

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