Variant report

Variant	rs2517459
Chromosome Location	chr6:30897022-30897023
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30882885..30885102-chr6:30895534..30897126,2	MCF-7	breast:
2	chr6:30895904..30897988-chr6:30898717..30900643,2	MCF-7	breast:
3	chr6:30693361..30695767-chr6:30895208..30897558,2	K562	blood:
4	chr6:30896359..30898136-chr6:30906028..30908064,2	K562	blood:

Variant related genes	Relation type
ENSG00000252761	Chromatin interaction
ENSG00000196260	Chromatin interaction
ENSG00000137411	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1043483	0.81[EUR][1000 genomes]
rs11970154	0.81[AFR][1000 genomes]
rs2253705	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2253718	0.83[AMR][1000 genomes]
rs2532932	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3094108	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3094719	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3095345	0.82[ASN][1000 genomes]
rs3130779	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3130780	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3130788	0.88[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs3130797	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3131028	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs3131032	0.93[AFR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3131034	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3891155	0.87[AFR][1000 genomes]
rs56366011	0.88[AFR][1000 genomes]
rs58893284	0.85[AFR][1000 genomes]
rs6933400	0.87[AFR][1000 genomes]
rs6933909	0.87[AFR][1000 genomes]
rs885905	0.81[EUR][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	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
5	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
6	nsv1031677	chr6:30857542-30972865	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv525438	chr6:30864829-30933975	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2517459	HIST1H2BL	cis	parietal	SCAN
rs2517459	PRSS16	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30889400-30900000	Weak transcription	Small Intestine	intestine
2	chr6:30892600-30899600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr6:30894200-30898800	Weak transcription	NHLF	lung
4	chr6:30894800-30897200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr6:30894800-30897200	Weak transcription	Colonic Mucosa	Colon
6	chr6:30894800-30897200	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr6:30894800-30897400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:30894800-30897400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr6:30894800-30898000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr6:30894800-30898200	Weak transcription	Gastric	stomach
11	chr6:30894800-30898800	Weak transcription	Fetal Lung	lung
12	chr6:30894800-30899200	Weak transcription	Fetal Intestine Large	intestine
13	chr6:30894800-30901000	Weak transcription	Fetal Kidney	kidney
14	chr6:30894800-30902600	Weak transcription	NHEK	skin
15	chr6:30894800-30903000	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr6:30894800-30905000	Weak transcription	Right Ventricle	heart
17	chr6:30895000-30897400	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr6:30895000-30899800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:30895400-30897200	Weak transcription	Ovary	ovary
20	chr6:30895400-30897800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr6:30895400-30899800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr6:30895600-30897400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr6:30895600-30897400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr6:30896000-30899000	Weak transcription	HUVEC	blood vessel
25	chr6:30896000-30904400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr6:30896200-30897200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr6:30896200-30897200	ZNF genes & repeats	Fetal Intestine Small	intestine
28	chr6:30896400-30897200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr6:30896400-30897200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr6:30896600-30905800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr6:30896800-30898000	Weak transcription	GM12878-XiMat	blood
32	chr6:30896800-30898200	Weak transcription	Esophagus	oesophagus
33	chr6:30896800-30899200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr6:30897000-30898400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr6:30897000-30899400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr6:30897000-30899600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:30897000-30899800	Weak transcription	HMEC	breast
38	chr6:30897000-30900000	Weak transcription	Pancreas	Pancrea
39	chr6:30897000-30900200	Weak transcription	A549	lung
40	chr6:30897000-30904000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:30897000-30905600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr6:30897000-30905800	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr6:30897000-30909800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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