Variant report

Variant	rs6456799
Chromosome Location	chr6:27573536-27573537
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:27573292..27575070-chr6:27575165..27577437,2	K562	blood:
2	chr6:27571900..27575468-chr6:27575673..27580181,6	K562	blood:
3	chr6:27156508..27159438-chr6:27571250..27573740,2	K562	blood:
4	chr6:27113006..27116236-chr6:27571739..27573884,3	K562	blood:
5	chr6:27572695..27575241-chr6:27583548..27587742,4	K562	blood:
6	chr6:27572199..27574195-chr6:27584979..27586709,2	K562	blood:
7	chr6:27568112..27571226-chr6:27572842..27574899,3	K562	blood:
8	chr6:27572241..27575123-chr6:27648524..27650391,2	K562	blood:
9	chr6:27571986..27574077-chr6:27721944..27723509,2	K562	blood:
10	chr6:27113006..27115425-chr6:27571739..27573552,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000184825	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000197903	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1022486	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1033451	0.88[ASN][1000 genomes]
rs10807026	0.85[ASN][1000 genomes]
rs10807029	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10946935	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.92[YRI][hapmap];0.82[EUR][1000 genomes]
rs10946936	0.82[EUR][1000 genomes]
rs10946938	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10946940	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12208078	0.81[EUR][1000 genomes]
rs12215012	0.82[EUR][1000 genomes]
rs13201411	0.82[EUR][1000 genomes]
rs2056924	0.87[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap]
rs2064093	0.80[YRI][hapmap]
rs2294480	0.87[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2294481	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2393964	0.81[YRI][hapmap]
rs4272217	0.83[ASN][1000 genomes]
rs4713112	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4713113	0.85[ASN][1000 genomes]
rs4713120	0.86[JPT][hapmap]
rs62401383	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67734963	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6899903	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6908295	0.81[ASN][1000 genomes]
rs6915266	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.87[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6915987	0.83[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs6916878	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs6918038	0.84[ASN][1000 genomes]
rs6921256	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6933926	0.80[ASN][1000 genomes]
rs6934437	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs6934794	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap]
rs7761966	0.81[YRI][hapmap]
rs7764081	0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs7769662	0.88[ASN][1000 genomes]
rs7774939	0.85[ASN][1000 genomes]
rs7775817	0.86[ASN][1000 genomes]
rs9295747	0.84[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.81[MKK][hapmap]
rs9348772	0.88[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap]
rs9357042	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9366697	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9380007	0.86[CHD][hapmap];0.91[JPT][hapmap]
rs9393830	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9393831	0.83[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv830617	chr6:27424769-27598595	Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1030256	chr6:27477726-27605842	Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv1025862	chr6:27480227-27605321	Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv1017347	chr6:27483816-27605842	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv1025572	chr6:27487852-27604454	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv538167	chr6:27487852-27604454	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv883509	chr6:27492906-27586181	Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
9	nsv1018107	chr6:27503525-27596736	Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
10	nsv538168	chr6:27503525-27596736	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	nsv883510	chr6:27550712-27730064	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
12	nsv1023673	chr6:27570731-27688782	Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6456799	AL022393.7	cis	Muscle Skeletal	GTEx
rs6456799	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27569800-27574400	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr6:27570600-27576800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:27572200-27574200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:27572200-27574400	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr6:27572200-27574400	Active TSS	H1 Cell Line	embryonic stem cell
6	chr6:27572200-27574400	Active TSS	H9 Cell Line	embryonic stem cell
7	chr6:27572200-27574400	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr6:27572400-27573800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:27572400-27574200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:27572400-27574200	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr6:27572600-27573800	Active TSS	A549	lung
12	chr6:27572600-27574000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr6:27572600-27574200	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr6:27572600-27574200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr6:27572600-27574200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr6:27572600-27574200	Active TSS	HMEC	breast
17	chr6:27572800-27573600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:27572800-27573600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
19	chr6:27572800-27573600	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
20	chr6:27572800-27573600	Bivalent Enhancer	Brain Hippocampus Middle	brain
21	chr6:27572800-27573600	Bivalent/Poised TSS	Fetal Stomach	stomach
22	chr6:27572800-27573600	Active TSS	NHEK	skin
23	chr6:27572800-27573800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr6:27572800-27573800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:27572800-27573800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr6:27572800-27573800	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
27	chr6:27572800-27573800	Active TSS	NHDF-Ad	bronchial
28	chr6:27572800-27574000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr6:27572800-27574000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:27572800-27574000	Active TSS	Muscle Satellite Cultured Cells	--
31	chr6:27572800-27574000	Active TSS	HSMM	muscle
32	chr6:27572800-27574000	Active TSS	NHLF	lung
33	chr6:27572800-27574200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr6:27572800-27574200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr6:27572800-27574200	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
36	chr6:27572800-27574400	Active TSS	HUES64 Cell Line	embryonic stem cell
37	chr6:27573000-27573600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
38	chr6:27573000-27573600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr6:27573000-27573600	Bivalent/Poised TSS	Placenta	Placenta
40	chr6:27573000-27573600	Active TSS	K562	blood
41	chr6:27573000-27573800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr6:27573000-27573800	Active TSS	HSMMtube	muscle
43	chr6:27573000-27574000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr6:27573000-27574000	Active TSS	NH-A	brain
45	chr6:27573000-27574000	Flanking Active TSS	Osteobl	bone
46	chr6:27573000-27574200	Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr6:27573000-27574200	Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr6:27573200-27573600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr6:27573200-27573600	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr6:27573200-27573600	Bivalent Enhancer	Fetal Heart	heart

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