Variant report

Variant	rs11891625
Chromosome Location	chr2:86182258-86182259
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86112745..86122516-chr2:86175080..86185190,27	MCF-7	breast:
2	chr2:85957540..85958262-chr2:86182061..86182634,2	MCF-7	breast:
3	chr2:85820787..85822313-chr2:86179412..86182366,2	K562	blood:
4	chr2:86170585..86172715-chr2:86181758..86183932,2	MCF-7	breast:
5	chr2:86181209..86184209-chr2:86184954..86187247,3	K562	blood:
6	chr2:86135754..86137623-chr2:86180466..86183254,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232504	Chromatin interaction
ENSG00000115525	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10181091	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10181916	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10183118	0.84[EUR][1000 genomes]
rs10186005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10189191	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10198260	0.92[ASN][1000 genomes]
rs1020095	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11890514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12470643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12472588	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12476390	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12714161	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12714163	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12714164	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12714165	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13000793	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13397189	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1438153	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1438155	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1561330	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1866242	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866243	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1866245	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4346389	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4480982	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4514874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4832018	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4832020	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6547651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6706720	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6708525	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6713002	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6728146	0.80[EUR][1000 genomes]
rs6737454	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7597264	0.87[ASN][1000 genomes]
rs934830	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][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	nsv1001104	chr2:86182021-86271923	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv535807	chr2:86182021-86271923	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11891625	REEP1	cis	parietal	SCAN
rs11891625	IMMT	cis	uninvolved skin	skin_eQTL
rs11891625	IMMT	cis	lymphoblastoid	seeQTL
rs11891625	MRPL35	cis	parietal	SCAN
rs11891625	C2orf51	cis	cerebellum	SCAN
rs11891625	ST3GAL5	cis	cerebellum	SCAN
rs11891625	PTCD3	cis	cerebellum	SCAN
rs11891625	IMMT	cis	cerebellum	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86175000-86183600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr2:86178800-86188200	Enhancers	Fetal Muscle Leg	muscle
3	chr2:86179200-86183600	Enhancers	Pancreas	Pancrea
4	chr2:86179200-86183800	Enhancers	Stomach Mucosa	stomach
5	chr2:86180000-86183400	Enhancers	Fetal Muscle Trunk	muscle
6	chr2:86180200-86183000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr2:86180200-86187600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:86180600-86184200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr2:86180800-86182400	Enhancers	HepG2	liver
10	chr2:86180800-86184000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr2:86180800-86184400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:86180800-86188600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:86181000-86182400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:86181000-86183000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr2:86181000-86183600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr2:86181000-86183800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:86181000-86186600	Weak transcription	K562	blood
18	chr2:86181600-86182400	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr2:86181600-86182600	Enhancers	Liver	Liver
20	chr2:86181800-86182600	Flanking Active TSS	A549	lung
21	chr2:86181800-86184200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:86181800-86186200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr2:86182000-86182400	Weak transcription	Fetal Lung	lung
24	chr2:86182000-86183400	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr2:86182200-86182400	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr2:86182200-86182600	Enhancers	Esophagus	oesophagus
27	chr2:86182200-86182600	Enhancers	Rectal Mucosa Donor 29	rectum
28	chr2:86182200-86183400	Enhancers	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links