Variant report

Variant	rs2138397
Chromosome Location	chr2:86974049-86974050
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	GATA3	chr2:86974041-86974413	T-47D	breast:	n/a	n/a
2	CEBPB	chr2:86974010-86974291	HepG2	liver:	n/a	chr2:86974163-86974174
3	CEBPB	chr2:86974002-86974311	A549	lung:	n/a	chr2:86974163-86974174

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86850136..86852379-chr2:86973884..86976847,2	K562	blood:

Variant related genes	Relation type
RMND5A	TF binding region
ENSG00000249884	Chromatin interaction
ENSG00000239305	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1005834	0.80[JPT][hapmap];0.86[MEX][hapmap]
rs10186663	1.00[CEU][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs10201422	0.95[CEU][hapmap];0.81[GIH][hapmap]
rs1049457	0.95[CEU][hapmap]
rs1049458	0.95[CEU][hapmap];0.81[GIH][hapmap]
rs11889231	0.92[EUR][1000 genomes]
rs1193	0.95[CEU][hapmap];0.81[GIH][hapmap]
rs12477737	0.85[ASN][1000 genomes]
rs12613610	0.86[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs12623395	0.80[JPT][hapmap]
rs12988718	0.94[ASN][1000 genomes]
rs1850138	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs1878109	1.00[CEU][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs2063848	1.00[CEU][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap]
rs2138396	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2367378	0.95[CEU][hapmap];0.81[GIH][hapmap]
rs2887012	1.00[CEU][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs308921	0.81[ASN][1000 genomes]
rs36100635	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4240205	0.82[MEX][hapmap]
rs4832047	0.81[ASN][1000 genomes]
rs4832048	0.84[ASN][1000 genomes]
rs4832306	0.81[ASN][1000 genomes]
rs4832311	1.00[CEU][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap]
rs6711696	0.81[EUR][1000 genomes]
rs6711700	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6726451	0.95[CEU][hapmap];0.81[GIH][hapmap];0.81[EUR][1000 genomes]
rs6731890	1.00[CEU][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs6743139	0.82[MEX][hapmap]
rs7558827	0.90[CHB][hapmap]
rs7587730	0.89[AFR][1000 genomes]
rs7596943	0.92[EUR][1000 genomes]
rs9309636	1.00[CEU][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs9309637	1.00[CEU][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs9309638	1.00[CEU][hapmap];0.83[GIH][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs938486	0.90[CEU][hapmap];0.81[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv10063	chr2:86940988-87084360	Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1002420	chr2:86948835-87172715	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv874472	chr2:86961252-87071474	Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv1008817	chr2:86970406-87172715	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv961426	chr2:86970416-86974654	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	esv14382	chr2:86972214-87174121	Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv997982	chr2:86972834-87105864	Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
9	nsv1007746	chr2:86972834-87172715	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2138397	RMND5A	cis	uninvolved skin	skin_eQTL
rs2138397	SFTPB	cis	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86949000-86979600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr2:86962200-86975400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:86962200-86977000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr2:86965200-86978800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:86966800-86977200	Weak transcription	Osteobl	bone
6	chr2:86968600-86974800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:86968600-86993000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:86968600-86997600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:86968800-86975000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr2:86968800-86977000	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr2:86968800-86977000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr2:86968800-86978600	Weak transcription	Placenta	Placenta
13	chr2:86968800-86980400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:86969000-86974400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr2:86969000-86974600	Weak transcription	NHEK	skin
16	chr2:86969200-86975000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:86969200-86977400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr2:86969200-86986400	Strong transcription	Fetal Thymus	thymus
19	chr2:86969200-86997800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:86969400-86979000	Weak transcription	Ovary	ovary
21	chr2:86969400-86984400	Weak transcription	Fetal Heart	heart
22	chr2:86969400-86997800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr2:86969600-86974200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr2:86969600-86974600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr2:86969600-86977200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr2:86969600-86995400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:86969600-86995400	Weak transcription	Esophagus	oesophagus
28	chr2:86969800-86975000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr2:86969800-86975000	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr2:86969800-86977200	Weak transcription	Fetal Kidney	kidney
31	chr2:86969800-86978600	Weak transcription	HSMM	muscle
32	chr2:86970000-86974400	Weak transcription	Brain Anterior Caudate	brain
33	chr2:86970000-86974800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr2:86970000-86974800	Weak transcription	HMEC	breast
35	chr2:86970000-86976000	Weak transcription	Hela-S3	cervix
36	chr2:86970000-86979800	Weak transcription	Colonic Mucosa	Colon
37	chr2:86970000-86980200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr2:86970000-87002000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr2:86970200-86974400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:86970200-86974800	Strong transcription	Primary B cells from peripheral blood	blood
41	chr2:86970200-86974800	Strong transcription	Dnd41	blood
42	chr2:86970200-86976800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr2:86970400-86974600	Weak transcription	Colon Smooth Muscle	Colon
44	chr2:86970400-86975200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr2:86970400-86980600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr2:86970400-86995400	Weak transcription	Aorta	Aorta
47	chr2:86970600-86974400	Strong transcription	Primary hematopoietic stem cells	blood
48	chr2:86970800-86975000	Weak transcription	NH-A	brain
49	chr2:86971000-86974200	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr2:86971000-86974600	Strong transcription	Primary B cells from cord blood	blood

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