Variant report

Variant	rs11682000
Chromosome Location	chr2:73166585-73166586
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:73162556..73166677-chr2:73167380..73171144,3	MCF-7	breast:
2	chr2:73165807..73168503-chr2:73169231..73171045,2	K562	blood:
3	chr2:73142842..73144664-chr2:73166470..73169412,2	K562	blood:

Variant related genes	Relation type
ENSG00000135638	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10195562	0.83[CEU][hapmap]
rs11691393	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11692971	1.00[LWK][hapmap]
rs55815158	0.97[EUR][1000 genomes]
rs72846991	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72846993	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72846995	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532723	chr2:73088191-73219259	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv874266	chr2:73137991-73220138	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11682000	SFXN5	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73159800-73169600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr2:73159800-73170600	Weak transcription	Aorta	Aorta
3	chr2:73160000-73166600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr2:73161400-73210200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr2:73161800-73167200	Weak transcription	Spleen	Spleen
6	chr2:73162000-73167400	Weak transcription	Fetal Intestine Small	intestine
7	chr2:73162600-73167600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:73162600-73169400	Weak transcription	Primary monocytes fromperipheralblood	blood
9	chr2:73163600-73166800	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr2:73163800-73169400	Weak transcription	Lung	lung
11	chr2:73163800-73170400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr2:73164000-73171200	Weak transcription	Brain Germinal Matrix	brain
13	chr2:73164200-73179000	Weak transcription	Brain Hippocampus Middle	brain
14	chr2:73164400-73168600	Weak transcription	Liver	Liver
15	chr2:73164400-73182800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr2:73164400-73190600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr2:73164400-73192800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr2:73164400-73193000	Weak transcription	Ovary	ovary
19	chr2:73164400-73193600	Weak transcription	Brain Angular Gyrus	brain
20	chr2:73164600-73166800	Weak transcription	Fetal Intestine Large	intestine
21	chr2:73164600-73169200	Weak transcription	Gastric	stomach
22	chr2:73164600-73169400	Weak transcription	Right Ventricle	heart
23	chr2:73164800-73167400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:73164800-73167600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr2:73164800-73170200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr2:73165000-73169000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr2:73165000-73175800	Weak transcription	Esophagus	oesophagus
28	chr2:73165400-73167000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr2:73165400-73170600	Weak transcription	Adipose Nuclei	Adipose
30	chr2:73165600-73167600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr2:73165800-73167200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr2:73165800-73167400	Weak transcription	Osteobl	bone
33	chr2:73166000-73169000	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr2:73166200-73167200	Weak transcription	Fetal Brain Female	brain
35	chr2:73166200-73167400	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr2:73166200-73169400	Weak transcription	Fetal Brain Male	brain
37	chr2:73166200-73170000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:73166200-73170200	Weak transcription	Brain Anterior Caudate	brain
39	chr2:73166200-73210000	Weak transcription	Colonic Mucosa	Colon
40	chr2:73166400-73167400	Weak transcription	NH-A	brain
41	chr2:73166400-73170200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links