Variant report

Variant	rs2759328
Chromosome Location	chr1:173876705-173876706
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:173875025..173877652-chr1:173913982..173916465,2	K562	blood:
2	chr1:173836150..173838914-chr1:173876553..173878764,2	MCF-7	breast:
3	chr1:173876474..173879309-chr1:173881795..173883444,2	K562	blood:
4	chr1:173872283..173875090-chr1:173876429..173879185,2	K562	blood:
5	chr1:173868704..173870321-chr1:173875152..173876806,2	K562	blood:

Variant related genes	Relation type
ENSG00000185278	Chromatin interaction
ENSG00000234741	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs16846418	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16846433	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16846478	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16846526	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846593	1.00[ASW][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2065170	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2068871	1.00[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2146372	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2227589	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2227592	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2235095	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3791021	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3791022	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs57022387	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58994962	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59393482	0.88[AMR][1000 genomes]
rs60689957	0.88[AMR][1000 genomes]
rs61262741	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61649485	0.84[ASN][1000 genomes]
rs6656255	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6685043	1.00[ASW][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs6691053	0.82[CHB][hapmap]
rs6696381	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6790	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs941987	1.00[ASW][hapmap];0.87[CEU][hapmap];0.88[GIH][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs941988	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9970048	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv831926	chr1:173702403-173894667	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	291 gene(s)	inside rSNPs	diseases
3	esv2757761	chr1:173810642-173955943	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
4	esv2758978	chr1:173810642-173955943	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2759328	CENPL	cis	lymphoblastoid	seeQTL
rs2759328	SNORD78	cis	parietal	SCAN
rs2759328		cis	Lymphoblastoid	GTEx
rs2759328	SNORD79	cis	parietal	SCAN
rs2759328	dJ383J4.3	cis	multi-tissue	Pritchard
rs2759328	SNORD80	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173855800-173880400	Weak transcription	Thymus	Thymus
2	chr1:173856000-173883000	Weak transcription	Right Ventricle	heart
3	chr1:173856200-173878400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr1:173856200-173880400	Weak transcription	Psoas Muscle	Psoas
5	chr1:173856400-173880000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr1:173856600-173881200	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr1:173856600-173907200	Weak transcription	Brain Germinal Matrix	brain
8	chr1:173857000-173883800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr1:173857400-173880400	Weak transcription	Fetal Brain Female	brain
10	chr1:173857400-173881800	Weak transcription	Brain Hippocampus Middle	brain
11	chr1:173857400-173884400	Weak transcription	HepG2	liver
12	chr1:173857400-173885800	Weak transcription	Fetal Intestine Large	intestine
13	chr1:173857400-173902000	Weak transcription	HSMMtube	muscle
14	chr1:173858200-173902800	Weak transcription	Left Ventricle	heart
15	chr1:173858400-173878600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr1:173858600-173881400	Weak transcription	Primary B cells from cord blood	blood
17	chr1:173858600-173886800	Weak transcription	Placenta	Placenta
18	chr1:173862000-173891600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr1:173863800-173878800	Weak transcription	Aorta	Aorta
20	chr1:173864200-173878600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:173864600-173878200	Weak transcription	Primary B cells from peripheral blood	blood
22	chr1:173864600-173886600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:173866600-173878600	Strong transcription	Liver	Liver
24	chr1:173869000-173880200	Weak transcription	Brain Angular Gyrus	brain
25	chr1:173869200-173880200	Weak transcription	Brain Substantia Nigra	brain
26	chr1:173869800-173877800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr1:173870000-173880400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:173870000-173898000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr1:173870200-173880600	Weak transcription	Adipose Nuclei	Adipose
30	chr1:173870400-173887400	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr1:173871200-173908400	Weak transcription	Spleen	Spleen
32	chr1:173871400-173879400	Weak transcription	Colon Smooth Muscle	Colon
33	chr1:173872200-173880200	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr1:173872200-173880800	Weak transcription	Fetal Stomach	stomach
35	chr1:173872400-173896200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr1:173873600-173880600	Weak transcription	Ovary	ovary
37	chr1:173874400-173899800	Weak transcription	Primary T cells from cord blood	blood
38	chr1:173876400-173884000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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