Variant report

Variant	rs4310524
Chromosome Location	chr10:6171924-6171925
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:6170183..6172118-chr10:6243569..6246358,3	MCF-7	breast:
2	chr10:6171306..6174580-chr10:6176089..6182503,5	MCF-7	breast:
3	chr10:6164842..6170645-chr10:6170879..6175262,7	K562	blood:
4	chr10:6171733..6174384-chr10:6244716..6246258,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170525	Chromatin interaction
ENSG00000213994	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10795840	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4237412	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4291579	0.88[EUR][1000 genomes]
rs5014463	0.89[EUR][1000 genomes]
rs5017841	0.88[EUR][1000 genomes]
rs7477416	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34061	chr10:5726821-6225187	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv1040721	chr10:6155144-6322566	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv540476	chr10:6155144-6322566	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv1054044	chr10:6155144-6487217	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4310524	PFKP	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6157600-6172000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr10:6159400-6172000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr10:6167000-6172000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr10:6167600-6172200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr10:6167600-6174800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr10:6168200-6178200	Weak transcription	A549	lung
7	chr10:6168600-6172000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr10:6168800-6172400	Enhancers	Spleen	Spleen
9	chr10:6169600-6172200	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr10:6170000-6172200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr10:6170000-6172400	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr10:6170000-6172400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr10:6170000-6172400	Enhancers	Fetal Lung	lung
14	chr10:6170000-6172400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr10:6170200-6172000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr10:6170200-6172400	Enhancers	Primary T cells from cord blood	blood
17	chr10:6170200-6173000	Enhancers	Fetal Thymus	thymus
18	chr10:6170200-6173200	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr10:6170200-6173200	Enhancers	GM12878-XiMat	blood
20	chr10:6170400-6172000	Enhancers	NHEK	skin
21	chr10:6170400-6172200	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr10:6170400-6172200	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr10:6170400-6172200	Enhancers	Thymus	Thymus
24	chr10:6170400-6172400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr10:6170400-6173200	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr10:6170400-6173400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
27	chr10:6170400-6173600	Enhancers	NH-A	brain
28	chr10:6170600-6173200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr10:6170600-6173400	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr10:6170800-6172000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr10:6170800-6172000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr10:6170800-6172200	Enhancers	Gastric	stomach
33	chr10:6170800-6172200	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr10:6170800-6173400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr10:6171000-6172000	Weak transcription	Brain Anterior Caudate	brain
36	chr10:6171000-6172400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr10:6171000-6172400	Enhancers	Placenta	Placenta
38	chr10:6171000-6172400	Enhancers	Lung	lung
39	chr10:6171000-6173000	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr10:6171200-6172000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr10:6171200-6172000	Weak transcription	HUVEC	blood vessel
42	chr10:6171200-6172200	Enhancers	Brain Cingulate Gyrus	brain
43	chr10:6171200-6172200	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr10:6171200-6172200	Enhancers	Ovary	ovary
45	chr10:6171200-6172400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr10:6171200-6172400	Enhancers	Esophagus	oesophagus
47	chr10:6171200-6173400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr10:6171200-6173400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr10:6171200-6173600	Enhancers	NHLF	lung
50	chr10:6171200-6174200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links