Variant report

Variant	rs16987398
Chromosome Location	chr2:20342501-20342502
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20342469..20346864-chr2:20382569..20386022,5	MCF-7	breast:
2	chr2:20337846..20345492-chr2:20421951..20427912,20	MCF-7	breast:
3	chr2:20340564..20344464-chr2:20412010..20415688,4	MCF-7	breast:
4	chr2:20313769..20315604-chr2:20340680..20342893,2	MCF-7	breast:
5	chr2:20335576..20338444-chr2:20340414..20343314,2	MCF-7	breast:
6	chr2:20338664..20345614-chr2:20377409..20381353,9	MCF-7	breast:
7	chr2:20341298..20344262-chr2:20354699..20358501,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213729	Chromatin interaction
ENSG00000115884	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12612001	0.81[EUR][1000 genomes]
rs12991571	0.86[MEX][hapmap];0.83[AMR][1000 genomes]
rs16987405	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16987429	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4666296	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4666363	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4666367	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4666371	0.83[AMR][1000 genomes]
rs56736615	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7583442	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009521	chr2:20310479-20388959	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1012841	chr2:20328894-20415168	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1012055	chr2:20336237-20356606	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1004083	chr2:20336237-20388138	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1000323	chr2:20336237-20419923	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats 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	15 gene(s)	inside rSNPs	diseases
6	nsv1004947	chr2:20342264-20388138	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16987398	RND3	trans	lymphoblastoid	seeQTL
rs16987398	LPAR6	trans	lymphoblastoid	seeQTL
rs16987398	UMODL1	trans	lymphoblastoid	seeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20332200-20364400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:20334200-20346600	Enhancers	Placenta	Placenta
3	chr2:20335800-20343400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:20336400-20346200	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr2:20337400-20343400	Enhancers	NHEK	skin
6	chr2:20338000-20345200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:20338000-20346800	Enhancers	HMEC	breast
8	chr2:20339600-20349200	Weak transcription	Small Intestine	intestine
9	chr2:20339800-20348200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr2:20340000-20345200	Weak transcription	Fetal Lung	lung
11	chr2:20340000-20348000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:20340000-20348400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr2:20340200-20342800	Weak transcription	Fetal Intestine Small	intestine
14	chr2:20340200-20348400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr2:20340600-20343200	Enhancers	Esophagus	oesophagus
16	chr2:20340600-20343400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:20340800-20347200	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr2:20341000-20344800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr2:20341200-20344800	Weak transcription	Colonic Mucosa	Colon
20	chr2:20341200-20345200	Weak transcription	Left Ventricle	heart
21	chr2:20341400-20344800	Weak transcription	Spleen	Spleen
22	chr2:20341400-20345000	Weak transcription	Duodenum Mucosa	Duodenum
23	chr2:20341400-20345200	Weak transcription	HSMMtube	muscle
24	chr2:20341400-20345400	Weak transcription	Right Ventricle	heart
25	chr2:20341400-20345600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr2:20341600-20342600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr2:20341600-20345200	Weak transcription	K562	blood
28	chr2:20341600-20345600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:20341800-20344000	Enhancers	A549	lung
30	chr2:20341800-20345000	Weak transcription	Liver	Liver
31	chr2:20341800-20348600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:20341800-20348600	Weak transcription	Adipose Nuclei	Adipose
33	chr2:20341800-20348800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr2:20342000-20343000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:20342000-20343000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr2:20342000-20344200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr2:20342000-20344600	Weak transcription	HUVEC	blood vessel
38	chr2:20342000-20346200	Weak transcription	Osteobl	bone
39	chr2:20342000-20346400	Weak transcription	NHDF-Ad	bronchial
40	chr2:20342000-20348000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:20342000-20348200	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr2:20342000-20348400	Weak transcription	NHLF	lung
43	chr2:20342000-20348600	Weak transcription	Hela-S3	cervix
44	chr2:20342200-20342600	Weak transcription	NH-A	brain
45	chr2:20342200-20343400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr2:20342400-20342800	Weak transcription	Stomach Mucosa	stomach
47	chr2:20342400-20343400	Enhancers	Fetal Intestine Large	intestine
48	chr2:20342400-20343400	Enhancers	Placenta Amnion	Placenta Amnion
49	chr2:20342400-20343600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links