Variant report

Variant	rs7594864
Chromosome Location	chr2:10537316-10537317
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:10535680..10537760-chr2:10586889..10589133,2	K562	blood:
2	chr2:10535464..10537756-chr2:10546210..10548957,2	K562	blood:
3	chr2:10535204..10537517-chr2:10547562..10550495,2	MCF-7	breast:
4	chr2:10427792..10430069-chr2:10536723..10539558,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000206633	Chromatin interaction
ENSG00000115758	Chromatin interaction
ENSG00000257135	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11676661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11688771	0.87[ASN][1000 genomes]
rs2270302	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3771124	0.82[ASN][1000 genomes]
rs3771125	0.82[ASN][1000 genomes]
rs3771127	0.81[ASN][1000 genomes]
rs3771130	0.90[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs3771139	0.82[ASN][1000 genomes]
rs56044909	0.82[ASN][1000 genomes]
rs6741475	0.99[EUR][1000 genomes]
rs7580442	0.88[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs7580561	1.00[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap];0.80[YRI][hapmap];0.89[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs7582990	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[GIH][hapmap];0.95[LWK][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs9917245	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530829	chr2:10357105-10655131	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
2	nsv873641	chr2:10480415-10544640	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv873643	chr2:10535481-10583160	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7594864	SLC27A3	trans	cerebellum	SCAN
rs7594864	RNF144A	cis	parietal	SCAN
rs7594864	HPCAL1	cis	multi-tissue	Pritchard

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10523000-10541000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:10523400-10537800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr2:10523600-10539000	Weak transcription	Thymus	Thymus
4	chr2:10526800-10537400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr2:10527200-10542400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr2:10530000-10540800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr2:10530400-10537600	Weak transcription	Psoas Muscle	Psoas
8	chr2:10530400-10538800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr2:10530400-10540800	Weak transcription	Colon Smooth Muscle	Colon
10	chr2:10530600-10539800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr2:10530600-10544400	Weak transcription	Brain Angular Gyrus	brain
12	chr2:10531000-10539800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:10531000-10540600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr2:10531000-10542400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:10531000-10544600	Weak transcription	NHLF	lung
16	chr2:10531200-10539800	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr2:10531200-10542400	Weak transcription	HSMMtube	muscle
18	chr2:10531200-10542400	Weak transcription	NH-A	brain
19	chr2:10531200-10544200	Weak transcription	Brain Substantia Nigra	brain
20	chr2:10531400-10539800	Weak transcription	HSMM	muscle
21	chr2:10531400-10541600	Weak transcription	Osteobl	bone
22	chr2:10532800-10537800	Enhancers	Primary T cells fromperipheralblood	blood
23	chr2:10533000-10540200	Weak transcription	Stomach Smooth Muscle	stomach
24	chr2:10533000-10551800	Weak transcription	Ovary	ovary
25	chr2:10533400-10549200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr2:10533600-10538400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr2:10533600-10539800	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr2:10533600-10539800	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr2:10533600-10544200	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr2:10533600-10544200	Weak transcription	Fetal Brain Female	brain
31	chr2:10533800-10537400	Weak transcription	Fetal Muscle Leg	muscle
32	chr2:10533800-10537600	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr2:10533800-10537800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr2:10533800-10538200	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr2:10533800-10538600	Weak transcription	Fetal Intestine Large	intestine
36	chr2:10533800-10538800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr2:10533800-10539400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr2:10533800-10539800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr2:10533800-10539800	Weak transcription	Colonic Mucosa	Colon
40	chr2:10533800-10539800	Weak transcription	Right Atrium	heart
41	chr2:10533800-10539800	Weak transcription	HepG2	liver
42	chr2:10534000-10537400	Weak transcription	Adipose Nuclei	Adipose
43	chr2:10534000-10537600	Weak transcription	Liver	Liver
44	chr2:10534000-10537600	Weak transcription	HUVEC	blood vessel
45	chr2:10534000-10538000	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr2:10534000-10538000	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr2:10534000-10538000	Weak transcription	A549	lung
48	chr2:10534000-10538200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr2:10534000-10538800	Weak transcription	K562	blood
50	chr2:10534000-10539400	Weak transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links