Variant report

Variant	rs1579028
Chromosome Location	chr6:38659978-38659979
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:38648522..38651548-chr6:38659281..38662308,3	K562	blood:
2	chr6:38655259..38657070-chr6:38659864..38662017,2	K562	blood:
3	chr6:38654849..38657579-chr6:38658333..38661175,3	K562	blood:
4	chr6:38568689..38571683-chr6:38658193..38660563,2	K562	blood:

Variant related genes	Relation type
ENSG00000124767	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10947757	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1130534	0.98[ASN][1000 genomes]
rs1621483	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3799703	0.92[JPT][hapmap]
rs4711553	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs4711556	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4714173	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs4714174	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs57156564	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57204119	0.81[ASN][1000 genomes]
rs58749921	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59793635	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60262339	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925790	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs6931745	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6932648	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.99[ASN][1000 genomes]
rs7767791	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs7774234	0.82[AMR][1000 genomes]
rs7775968	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs9296255	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs9366969	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs9369073	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs9369075	0.98[ASN][1000 genomes]
rs937662	0.92[JPT][hapmap]
rs9380763	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs9394516	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs9394519	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs9394522	0.94[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs9394523	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9394524	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9462446	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs9462448	0.92[JPT][hapmap]
rs9462451	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9462453	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9470901	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs9470902	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs9470913	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9470916	1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9470917	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9470918	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	esv2758049	chr6:38588969-38711085	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	esv2759421	chr6:38588969-38711085	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv427754	chr6:38588969-38711085	Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv428144	chr6:38588969-38711085	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv830642	chr6:38645056-38800657	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38641200-38670000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:38641600-38668000	Weak transcription	NHLF	lung
3	chr6:38642400-38660000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:38642400-38665600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr6:38642800-38669800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr6:38646000-38670000	Weak transcription	A549	lung
7	chr6:38646600-38663400	Weak transcription	Esophagus	oesophagus
8	chr6:38646800-38668200	Weak transcription	Primary T cells from cord blood	blood
9	chr6:38648800-38669800	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr6:38650200-38663400	Weak transcription	HUVEC	blood vessel
11	chr6:38650200-38666600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr6:38650800-38666400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr6:38651000-38667800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr6:38651200-38665800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr6:38651200-38667800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr6:38651200-38668000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr6:38651200-38668000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr6:38651200-38669800	Weak transcription	HSMM	muscle
19	chr6:38651200-38670000	Weak transcription	Fetal Kidney	kidney
20	chr6:38651400-38669400	Weak transcription	Osteobl	bone
21	chr6:38652000-38666600	Weak transcription	Fetal Intestine Small	intestine
22	chr6:38652000-38668000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:38652200-38662200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr6:38652400-38668000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:38653000-38668000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr6:38653000-38670000	Weak transcription	NHDF-Ad	bronchial
27	chr6:38653600-38663200	Weak transcription	HMEC	breast
28	chr6:38653600-38669400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr6:38653800-38663200	Weak transcription	Dnd41	blood
30	chr6:38654000-38663600	Weak transcription	K562	blood
31	chr6:38654400-38669800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr6:38654600-38668000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr6:38654600-38668000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr6:38654600-38668000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr6:38654600-38669400	Weak transcription	Hela-S3	cervix
36	chr6:38655200-38662000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr6:38655200-38665000	Weak transcription	NHEK	skin
38	chr6:38655200-38666600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:38655200-38667400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr6:38655200-38669800	Weak transcription	Pancreas	Pancrea
41	chr6:38655200-38670000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr6:38655400-38668000	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr6:38655600-38662600	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr6:38655600-38668000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr6:38656800-38668000	Weak transcription	Fetal Stomach	stomach
46	chr6:38656800-38668000	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr6:38657000-38661800	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr6:38657000-38662200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr6:38657000-38663200	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr6:38657000-38663400	Weak transcription	Small Intestine	intestine

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