Variant report

Variant	rs2517576
Chromosome Location	chr6:30815035-30815036
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:30796590..30799414-chr6:30814456..30816508,2	K562	blood:
2	chr6:30814424..30817937-chr6:30849019..30852528,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204580	Chromatin interaction
ENSG00000214894	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10947109	0.81[ASN][1000 genomes]
rs11759918	0.92[ASN][1000 genomes]
rs1264318	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1264319	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17189749	0.81[ASN][1000 genomes]
rs17840009	0.92[ASN][1000 genomes]
rs2535333	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844657	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2844659	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2894054	0.83[ASN][1000 genomes]
rs45627239	0.81[ASN][1000 genomes]
rs55697712	0.81[ASN][1000 genomes]
rs59124304	0.81[ASN][1000 genomes]
rs6940037	0.81[ASN][1000 genomes]
rs73727104	0.81[ASN][1000 genomes]
rs73727106	0.81[ASN][1000 genomes]
rs73727107	0.89[ASN][1000 genomes]
rs73727480	0.83[ASN][1000 genomes]
rs7761138	0.89[ASN][1000 genomes]
rs7772269	0.92[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	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS 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	1012 gene(s)	inside rSNPs	diseases
4	esv2758041	chr6:30644693-30816319	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
5	esv2759413	chr6:30644693-30816319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
6	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
7	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2517576	HIST1H2AM	cis	cerebellum	SCAN
rs2517576	VARS2	cis	lymphoblastoid	seeQTL
rs2517576	C6orf1	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30806800-30816200	Enhancers	Placenta	Placenta
2	chr6:30812000-30815400	Enhancers	Thymus	Thymus
3	chr6:30812000-30816200	Enhancers	Fetal Thymus	thymus
4	chr6:30812400-30815200	Weak transcription	HMEC	breast
5	chr6:30812400-30817000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr6:30812400-30822600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:30812600-30815200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:30812600-30815200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr6:30812600-30815200	Weak transcription	Esophagus	oesophagus
10	chr6:30812600-30815200	Weak transcription	Fetal Lung	lung
11	chr6:30812600-30815400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:30812600-30820600	Weak transcription	Right Atrium	heart
13	chr6:30812800-30817000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:30813600-30815200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr6:30813600-30816000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:30814000-30815200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr6:30814000-30815400	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr6:30814000-30817000	Weak transcription	Fetal Intestine Small	intestine
19	chr6:30814400-30815800	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr6:30814600-30815800	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr6:30814600-30816200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:30814800-30815200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr6:30814800-30815200	Enhancers	Placenta Amnion	Placenta Amnion
24	chr6:30814800-30815400	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr6:30814800-30815800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr6:30814800-30815800	Enhancers	HepG2	liver
27	chr6:30814800-30816200	Active TSS	H9 Cell Line	embryonic stem cell
28	chr6:30814800-30816200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr6:30814800-30816200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr6:30814800-30816200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:30814800-30816200	Enhancers	Fetal Kidney	kidney
32	chr6:30814800-30816400	Enhancers	NHEK	skin
33	chr6:30814800-30816600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr6:30814800-30817600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr6:30815000-30815200	Active TSS	H1 Cell Line	embryonic stem cell
36	chr6:30815000-30815400	Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr6:30815000-30815400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr6:30815000-30815400	Enhancers	Adipose Nuclei	Adipose
39	chr6:30815000-30816000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr6:30815000-30816200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr6:30815000-30816600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:30815000-30816600	Enhancers	Fetal Heart	heart

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