Variant report

Variant	rs35480652
Chromosome Location	chr2:234256849-234256850
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:234255807..234258253-chr2:234261320..234263742,3	MCF-7	breast:
2	chr2:234253774..234256883-chr2:234262038..234267744,5	K562	blood:

Variant related genes	Relation type
ENSG00000243637	Chromatin interaction
ENSG00000259793	Chromatin interaction
ENSG00000077044	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1046974	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10803624	0.95[ASN][1000 genomes]
rs10803625	0.82[ASN][1000 genomes]
rs11676156	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11679046	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11681192	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11682579	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13002340	0.83[ASN][1000 genomes]
rs13003198	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2879924	0.95[ASN][1000 genomes]
rs2879925	0.94[ASN][1000 genomes]
rs34595600	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34891595	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3828305	0.95[ASN][1000 genomes]
rs67399374	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7423426	0.95[ASN][1000 genomes]
rs880114	0.95[ASN][1000 genomes]
rs880116	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv584700	chr2:234199401-234364426	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv1002075	chr2:234225979-234277508	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
4	nsv460135	chr2:234242347-234288048	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv584701	chr2:234242347-234288048	ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv460136	chr2:234244395-234288048	Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv584702	chr2:234244395-234288048	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35480652	DGKD	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234244600-234257800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr2:234247600-234257400	Weak transcription	Spleen	Spleen
3	chr2:234249400-234257000	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr2:234255000-234257800	Enhancers	Brain Cingulate Gyrus	brain
5	chr2:234255000-234260000	Enhancers	Liver	Liver
6	chr2:234255400-234257600	Enhancers	Brain Anterior Caudate	brain
7	chr2:234255600-234258600	Enhancers	Brain Substantia Nigra	brain
8	chr2:234255800-234258600	Flanking Active TSS	HepG2	liver
9	chr2:234255800-234262400	Weak transcription	Right Atrium	heart
10	chr2:234256000-234257600	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr2:234256000-234257800	Weak transcription	K562	blood
12	chr2:234256200-234260800	Enhancers	Primary B cells from peripheral blood	blood
13	chr2:234256400-234260400	Enhancers	Fetal Intestine Small	intestine
14	chr2:234256400-234262400	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr2:234256600-234257000	Bivalent Enhancer	Fetal Muscle Leg	muscle
16	chr2:234256600-234257400	Enhancers	Rectal Mucosa Donor 29	rectum
17	chr2:234256600-234257800	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr2:234256600-234259800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:234256600-234261400	Enhancers	Primary B cells from cord blood	blood
20	chr2:234256800-234257000	Flanking Active TSS	Duodenum Mucosa	Duodenum
21	chr2:234256800-234257600	Enhancers	Brain Hippocampus Middle	brain
22	chr2:234256800-234257800	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr2:234256800-234258000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:234256800-234258400	Enhancers	Gastric	stomach
25	chr2:234256800-234258800	Enhancers	Brain Angular Gyrus	brain
26	chr2:234256800-234262400	Enhancers	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links