Variant report

Variant	rs2175225
Chromosome Location	chr15:99869197-99869198
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr15:99868473-99869258	HepG2	liver:	n/a	chr15:99869071-99869082
2	JUND	chr15:99868929-99869210	HepG2	liver:	n/a	n/a
3	CEBPB	chr15:99868962-99869204	H1-hESC	embryonic stem cell:	n/a	chr15:99869071-99869082
4	CEBPB	chr15:99868912-99869225	HepG2	liver:	n/a	chr15:99869071-99869082

Variant related genes	Relation type
LRRC28	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1033035	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1033036	0.94[ASN][1000 genomes]
rs11247079	0.80[ASN][1000 genomes]
rs11247081	0.94[ASN][1000 genomes]
rs12591088	0.83[JPT][hapmap]
rs12592717	0.83[JPT][hapmap]
rs12912927	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1472988	0.83[JPT][hapmap]
rs1472989	0.94[ASN][1000 genomes]
rs1876927	0.94[ASN][1000 genomes]
rs2048305	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28520505	0.97[ASN][1000 genomes]
rs3851679	0.93[ASN][1000 genomes]
rs3863401	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58946939	0.91[ASN][1000 genomes]
rs6598237	0.96[ASN][1000 genomes]
rs7167119	0.84[ASN][1000 genomes]
rs7167542	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7167899	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7168227	0.92[ASN][1000 genomes]
rs7169906	0.96[ASN][1000 genomes]
rs7171970	0.96[ASN][1000 genomes]
rs7173844	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7182425	0.93[ASN][1000 genomes]
rs7498053	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8038970	0.85[EUR][1000 genomes]
rs8040850	0.84[ASN][1000 genomes]
rs8042249	0.80[ASN][1000 genomes]
rs8042667	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531079	chr15:98907913-99878547	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv1039575	chr15:98982045-99924685	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv869529	chr15:99416774-99903351	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv904543	chr15:99513231-99991506	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv533926	chr15:99519820-99997114	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	nsv916822	chr15:99621061-99878564	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
9	nsv949203	chr15:99621061-99932797	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
10	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
11	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
12	nsv570716	chr15:99629901-99916332	Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
13	nsv904546	chr15:99696046-100166300	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
14	nsv1052528	chr15:99736977-99874210	Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
15	nsv1036346	chr15:99752391-100365458	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
16	nsv542520	chr15:99752391-100365458	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
17	nsv1045367	chr15:99781626-99892182	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
18	nsv1051560	chr15:99837102-100124483	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
19	nsv817201	chr15:99839238-100537341	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99833200-99875800	Weak transcription	Thymus	Thymus
2	chr15:99847400-99877200	Weak transcription	Ovary	ovary
3	chr15:99853000-99876000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr15:99853200-99875400	Weak transcription	Fetal Thymus	thymus
5	chr15:99853600-99875800	Weak transcription	Fetal Intestine Large	intestine
6	chr15:99854400-99876000	Weak transcription	Dnd41	blood
7	chr15:99858600-99876600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr15:99859400-99906600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr15:99860600-99869200	Enhancers	HepG2	liver
10	chr15:99861800-99876600	Weak transcription	Primary T cells from cord blood	blood
11	chr15:99863200-99881200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr15:99863200-99899800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr15:99864400-99902200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr15:99864600-99877200	Weak transcription	Fetal Muscle Leg	muscle
15	chr15:99864800-99881400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr15:99864800-99884200	Weak transcription	Primary B cells from peripheral blood	blood
17	chr15:99865200-99870800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr15:99865200-99875800	Weak transcription	Adipose Nuclei	Adipose
19	chr15:99865200-99880600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr15:99865400-99870800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr15:99866200-99869600	Weak transcription	GM12878-XiMat	blood
22	chr15:99866800-99871600	Weak transcription	HSMMtube	muscle
23	chr15:99866800-99875600	Weak transcription	Left Ventricle	heart
24	chr15:99866800-99875800	Weak transcription	Pancreas	Pancrea
25	chr15:99866800-99877400	Weak transcription	Right Ventricle	heart
26	chr15:99866800-99877800	Weak transcription	Psoas Muscle	Psoas
27	chr15:99866800-99881000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr15:99866800-99882400	Weak transcription	Gastric	stomach
29	chr15:99867000-99871200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr15:99867000-99880600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr15:99867200-99869800	Enhancers	A549	lung
32	chr15:99867200-99877400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr15:99867200-99926600	Weak transcription	NHEK	skin
34	chr15:99868400-99869200	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr15:99868400-99869200	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr15:99868600-99875800	Weak transcription	Liver	Liver
37	chr15:99869000-99877200	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links