Variant report

Variant	rs7411708
Chromosome Location	chr1:165726278-165726279
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:165724083..165726659-chr1:165795970..165798068,3	K562	blood:
2	chr1:165724083..165728644-chr1:165795970..165799220,7	K562	blood:
3	chr1:165719684..165722558-chr1:165723344..165727845,5	K562	blood:
4	chr1:165725229..165727213-chr1:165796804..165799182,3	MCF-7	breast:
5	chr1:165720854..165729861-chr1:165736355..165740477,8	K562	blood:

Variant related genes	Relation type
ENSG00000143183	Chromatin interaction
ENSG00000224358	Chromatin interaction
ENSG00000143179	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10800152	0.90[CHB][hapmap]
rs10918266	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10918276	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10918281	0.90[CHB][hapmap]
rs12028087	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12723198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs14223	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1913846	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2153263	0.82[CHD][hapmap]
rs2153264	0.82[CHD][hapmap]
rs2814470	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4656462	0.90[CHB][hapmap]
rs4657470	0.88[CEU][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs6426937	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6426940	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6656194	0.80[CHB][hapmap]
rs6670705	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7512095	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7540840	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[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	esv2756102	chr1:165652342-165877342	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1011720	chr1:165669589-165802516	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv518886	chr1:165714187-165741646	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7411708	FCGR3A	cis	parietal	SCAN
rs7411708	ARHGAP30	cis	parietal	SCAN
rs7411708	ADCY10	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165687600-165737600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:165694600-165736800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:165710400-165727000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:165711200-165736200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:165712200-165737000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:165712400-165726800	Weak transcription	Fetal Lung	lung
7	chr1:165712400-165727000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:165712400-165727200	Weak transcription	HMEC	breast
9	chr1:165712600-165737000	Weak transcription	Colonic Mucosa	Colon
10	chr1:165713400-165733600	Weak transcription	NHEK	skin
11	chr1:165713600-165737000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:165716800-165728000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr1:165717400-165728000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:165720800-165733400	Weak transcription	A549	lung
15	chr1:165721800-165726800	Weak transcription	Aorta	Aorta
16	chr1:165721800-165727200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr1:165721800-165727200	Weak transcription	Right Ventricle	heart
18	chr1:165721800-165728800	Weak transcription	Brain Substantia Nigra	brain
19	chr1:165721800-165728800	Strong transcription	Fetal Intestine Large	intestine
20	chr1:165721800-165729200	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr1:165721800-165730800	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr1:165721800-165731000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:165721800-165731200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:165721800-165732600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr1:165721800-165732600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr1:165721800-165732600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr1:165721800-165732800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr1:165721800-165732800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr1:165721800-165734800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr1:165721800-165734800	Weak transcription	Brain Cingulate Gyrus	brain
31	chr1:165721800-165734800	Weak transcription	Esophagus	oesophagus
32	chr1:165721800-165735200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr1:165721800-165736600	Weak transcription	Stomach Mucosa	stomach
34	chr1:165721800-165737000	Weak transcription	Fetal Brain Male	brain
35	chr1:165721800-165737000	Weak transcription	Fetal Heart	heart
36	chr1:165721800-165737000	Weak transcription	Right Atrium	heart
37	chr1:165721800-165737200	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr1:165721800-165737600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr1:165722000-165727800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:165722400-165732800	Weak transcription	HepG2	liver
41	chr1:165722400-165735000	Weak transcription	HSMMtube	muscle
42	chr1:165722600-165727200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr1:165722600-165733400	Weak transcription	Brain Anterior Caudate	brain
44	chr1:165722600-165733600	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr1:165722600-165736800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:165722800-165729200	Strong transcription	Fetal Kidney	kidney
47	chr1:165722800-165734800	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr1:165723000-165726800	Weak transcription	Fetal Muscle Trunk	muscle
49	chr1:165723000-165726800	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr1:165723000-165727400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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