Variant report

Variant	rs10280499
Chromosome Location	chr7:150453748-150453749
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:149981999..149984542-chr7:150453171..150454808,2	K562	blood:
2	chr7:150145471..150146422-chr7:150453633..150454441,6	MCF-7	breast:
3	chr7:150445779..150447547-chr7:150452187..150454363,2	K562	blood:
4	chr7:150143548..150144244-chr7:150453342..150454315,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241134	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11769454	1.00[ASN][1000 genomes]
rs11973400	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17173583	1.00[CHB][hapmap];0.87[YRI][hapmap];1.00[ASN][1000 genomes]
rs2058446	1.00[CHB][hapmap];0.87[YRI][hapmap];1.00[ASN][1000 genomes]
rs58313703	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58803836	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59004814	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66743416	1.00[ASN][1000 genomes]
rs6965571	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs741069	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9657879	1.00[CHB][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv608990	chr7:149961274-150707488	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv1017368	chr7:150016952-150655773	Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
3	nsv539195	chr7:150016952-150655773	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	esv2758617	chr7:150251949-150463804	Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	esv2759573	chr7:150251949-150463804	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv1030109	chr7:150312916-150701010	Enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	nsv967475	chr7:150323577-150610034	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv831187	chr7:150325913-150503500	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10280499	LR8	cis	multi-tissue	Pritchard
rs10280499	HCA112	cis	multi-tissue	Pritchard
rs10280499	GAP43	trans	lymphoblastoid	seeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:150442400-150454600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr7:150448800-150454200	Enhancers	Fetal Heart	heart
3	chr7:150449000-150454000	Enhancers	GM12878-XiMat	blood
4	chr7:150449400-150461000	Weak transcription	Liver	Liver
5	chr7:150450000-150453800	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr7:150450000-150453800	Enhancers	Primary hematopoietic stem cells	blood
7	chr7:150450000-150453800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr7:150450200-150454000	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr7:150451200-150454200	Enhancers	HUVEC	blood vessel
10	chr7:150451400-150453800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr7:150452200-150453800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
12	chr7:150452200-150454000	Flanking Active TSS	Primary T cells from cord blood	blood
13	chr7:150452200-150454000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
14	chr7:150452800-150454600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr7:150453000-150454400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr7:150453000-150454600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr7:150453200-150453800	Enhancers	Small Intestine	intestine
18	chr7:150453200-150454000	Enhancers	Monocytes-CD14+_RO01746	blood
19	chr7:150453400-150453800	Enhancers	Primary T cells fromperipheralblood	blood
20	chr7:150453400-150454600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr7:150453600-150453800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
22	chr7:150453600-150453800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr7:150453600-150454400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr7:150453600-150454600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr7:150453600-150454600	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr7:150453600-150454600	Enhancers	Dnd41	blood
27	chr7:150453600-150455000	Enhancers	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links