Variant report

Variant	rs2305814
Chromosome Location	chr1:150958977-150958978
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:150897536..150900393-chr1:150958359..150960737,2	K562	blood:
2	chr1:150952248..150956266-chr1:150957653..150962515,6	K562	blood:
3	chr1:150958810..150961134-chr1:151484440..151487024,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143412	Chromatin interaction
ENSG00000143379	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 32 )

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

rs_ID	r²[population]
rs11204752	0.98[ASN][1000 genomes]
rs11587718	0.95[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs11587720	0.91[ASN][1000 genomes]
rs1673160	0.90[CHB][hapmap];0.90[ASN][1000 genomes]
rs267735	0.84[ASN][1000 genomes]
rs3754211	0.85[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs486836	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs4970932	0.80[ASN][1000 genomes]
rs6587551	0.94[ASN][1000 genomes]
rs7532008	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap]
rs771201	0.90[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	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv1008496	chr1:150845827-150970656	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	nsv522317	chr1:150933723-150974162	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases

mRNA abundance (count:32)

SNP	Gene	Cis/trans	Tissue	Source
rs2305814	CTSK	cis	cerebellum	SCAN
rs2305814	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs2305814	ARNT	cis	lesional skin	skin_eQTL
rs2305814	ARNT	cis	uninvolved skin	skin_eQTL
rs2305814	HORMAD1	cis	normal skin	skin_eQTL
rs2305814	CTSS	cis	cerebellum	SCAN
rs2305814	RP11-316M1.12	cis	Whole Blood	GTEx
rs2305814	CTSS	cis	lymphoblastoid	seeQTL
rs2305814	ARNT	cis	normal skin	skin_eQTL
rs2305814	ARNT	cis	cerebellum	SCAN
rs2305814	CTSS	cis	parietal	SCAN
rs2305814	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs2305814	FLG	cis	cerebellum	SCAN
rs2305814	HORMAD1	cis	parietal	SCAN
rs2305814	HORMAD1	cis	uninvolved skin	skin_eQTL
rs2305814	ARNT	cis	parietal	SCAN
rs2305814	PLEKHO1	cis	cerebellum	SCAN
rs2305814	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs2305814	PSMD4	cis	parietal	SCAN
rs2305814	CTSK	cis	parietal	SCAN
rs2305814	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs2305814	HORMAD1	cis	Esophagus Mucosa	GTEx
rs2305814	ARNT	cis	Thyroid	GTEx
rs2305814	RP11-316M1.12	cis	lung	GTEx
rs2305814	RP11-316M1.12	cis	Artery Tibial	GTEx
rs2305814	HORMAD1	cis	Nerve Tibial	GTEx
rs2305814	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs2305814	HORMAD1	cis	lesional skin	skin_eQTL
rs2305814	RP11-316M1.12	cis	Esophagus Muscularis	GTEx
rs2305814	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs2305814	RP11-316M1.12	cis	Thyroid	GTEx
rs2305814	RP11-316M1.12	cis	Nerve Tibial	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150952000-150968000	Weak transcription	Spleen	Spleen
2	chr1:150952600-150960800	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr1:150952600-150968000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:150953600-150959000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:150954200-150969400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:150954800-150968000	Weak transcription	Fetal Kidney	kidney
7	chr1:150955000-150969400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr1:150955400-150969400	Weak transcription	Gastric	stomach
9	chr1:150955400-150970400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:150955400-150978800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:150955600-150967600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:150955600-150968200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:150955800-150967600	Weak transcription	Fetal Intestine Small	intestine
14	chr1:150956200-150969400	Weak transcription	Fetal Intestine Large	intestine
15	chr1:150957800-150967600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr1:150958000-150967600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:150958400-150967600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr1:150958600-150959200	Strong transcription	HepG2	liver
19	chr1:150958600-150961400	Strong transcription	Liver	Liver
20	chr1:150958800-150959000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:150958800-150959000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:150958800-150959200	Strong transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links