Variant report

Variant	rs16842142
Chromosome Location	chr3:100065577-100065578
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:100057175..100060153-chr3:100065543..100067180,2	K562	blood:
2	chr3:100053577..100055099-chr3:100063294..100065719,2	MCF-7	breast:
3	chr3:100064881..100067551-chr3:100115923..100118439,2	MCF-7	breast:
4	chr3:100057791..100061321-chr3:100063708..100069038,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114021	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10511179	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs11918399	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11919543	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11919627	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17279967	1.00[CHB][hapmap];0.84[CHD][hapmap]
rs3772687	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55699261	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55864663	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56012915	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56956506	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57155242	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57166766	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57332305	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57703319	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59304656	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59396265	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59491720	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59507591	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59509062	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60463428	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60999188	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72941434	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72941452	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72941453	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72941454	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72941473	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72941482	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9873033	1.00[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.81[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	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1003924	chr3:99933762-100112690	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100054200-100081000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:100054400-100067600	Weak transcription	Psoas Muscle	Psoas
3	chr3:100054600-100102600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:100054800-100067200	Weak transcription	Esophagus	oesophagus
5	chr3:100054800-100067400	Weak transcription	Small Intestine	intestine
6	chr3:100054800-100067600	Weak transcription	Colonic Mucosa	Colon
7	chr3:100054800-100068600	Weak transcription	Pancreas	Pancrea
8	chr3:100054800-100069000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:100054800-100081000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr3:100054800-100097200	Weak transcription	Stomach Mucosa	stomach
11	chr3:100054800-100102200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:100055000-100068200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr3:100055000-100068600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr3:100055000-100082400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr3:100055200-100068200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr3:100055200-100071000	Weak transcription	HepG2	liver
17	chr3:100057000-100069200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:100057000-100069600	Strong transcription	Dnd41	blood
19	chr3:100057200-100066800	Strong transcription	HSMM	muscle
20	chr3:100057200-100069200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:100057200-100069600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:100057400-100069600	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr3:100057600-100066200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:100057600-100069200	Strong transcription	Stomach Smooth Muscle	stomach
25	chr3:100057600-100069600	Strong transcription	Primary B cells from peripheral blood	blood
26	chr3:100057600-100069600	Strong transcription	Adipose Nuclei	Adipose
27	chr3:100057800-100066200	Strong transcription	HMEC	breast
28	chr3:100057800-100069600	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr3:100057800-100071400	Weak transcription	Fetal Heart	heart
30	chr3:100058000-100065800	Strong transcription	A549	lung
31	chr3:100058000-100069600	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr3:100058000-100069600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr3:100058000-100069600	Strong transcription	Skeletal Muscle Female	skeletal muscle
34	chr3:100058200-100065800	Strong transcription	Placenta	Placenta
35	chr3:100058200-100069600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:100058200-100069600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr3:100058400-100065800	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr3:100059200-100067600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:100059400-100069600	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr3:100060000-100069600	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr3:100060200-100067800	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr3:100060200-100068400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr3:100060200-100069600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:100060800-100066400	Weak transcription	Right Ventricle	heart
45	chr3:100061000-100067000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr3:100061000-100068600	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr3:100061000-100069000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:100061000-100069600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:100061000-100069600	Strong transcription	Liver	Liver
50	chr3:100061200-100066800	Weak transcription	Fetal Brain Female	brain

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