Variant report

Variant	rs58012164
Chromosome Location	chr2:47609342-47609343
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47607664..47610611-chr2:47628092..47629761,2	K562	blood:
2	chr2:47401083..47402908-chr2:47607249..47610060,2	K562	blood:
3	chr2:47606207..47609402-chr2:47613991..47616587,3	MCF-7	breast:
4	chr2:47599030..47603180-chr2:47606229..47610193,5	MCF-7	breast:
5	chr2:47595231..47597940-chr2:47605594..47609374,6	MCF-7	breast:
6	chr2:47595471..47599330-chr2:47606044..47611374,6	MCF-7	breast:
7	chr2:47608775..47611521-chr2:47612524..47615427,2	K562	blood:

Variant related genes	Relation type
ENSG00000119888	Chromatin interaction
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs17036586	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17036616	1.00[AMR][1000 genomes]
rs17039236	1.00[AMR][1000 genomes]
rs17217849	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17217961	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17218648	1.00[AMR][1000 genomes]
rs17224122	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17224724	1.00[AMR][1000 genomes]
rs17224738	1.00[AMR][1000 genomes]
rs17224815	1.00[AMR][1000 genomes]
rs1800151	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55815447	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55905016	1.00[AMR][1000 genomes]
rs56076616	1.00[AMR][1000 genomes]
rs56958162	1.00[AMR][1000 genomes]
rs56983268	1.00[AMR][1000 genomes]
rs57972954	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58080795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58930161	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59974084	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60121180	1.00[AMR][1000 genomes]
rs60512750	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61282650	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61635665	1.00[AMR][1000 genomes]
rs72882725	1.00[AMR][1000 genomes]
rs72882752	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72882765	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72882783	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72882786	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72882796	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72882802	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72884625	1.00[AMR][1000 genomes]
rs72884632	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72884676	1.00[AMR][1000 genomes]
rs72886304	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72886358	1.00[AMR][1000 genomes]
rs72888237	1.00[AMR][1000 genomes]
rs72888238	1.00[AMR][1000 genomes]
rs72888263	1.00[AMR][1000 genomes]
rs73927793	0.85[AFR][1000 genomes]
rs73927801	1.00[AMR][1000 genomes]
rs73927802	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv531348	chr2:47433147-47827310	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv999576	chr2:47506116-47773960	Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv1009586	chr2:47552706-47621487	Strong transcription Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47597200-47610600	Weak transcription	Right Atrium	heart
2	chr2:47597200-47615000	Weak transcription	Esophagus	oesophagus
3	chr2:47597200-47619800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:47597400-47614800	Weak transcription	HMEC	breast
5	chr2:47597400-47617000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:47597400-47629400	Weak transcription	NHEK	skin
7	chr2:47597600-47615400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:47598600-47613000	Weak transcription	Lung	lung
9	chr2:47600200-47617800	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr2:47600400-47616800	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr2:47600600-47614000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr2:47600600-47617200	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr2:47600800-47614000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr2:47601000-47610200	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr2:47601000-47610600	Strong transcription	H9 Cell Line	embryonic stem cell
16	chr2:47601000-47614200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:47601200-47609400	Weak transcription	Brain Anterior Caudate	brain
18	chr2:47601200-47614600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr2:47601200-47616800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr2:47601200-47629400	Weak transcription	Stomach Mucosa	stomach
21	chr2:47601400-47610400	Weak transcription	Fetal Lung	lung
22	chr2:47602600-47610200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr2:47603200-47619000	Weak transcription	K562	blood
24	chr2:47604800-47617000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:47604800-47628800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr2:47605200-47629000	Weak transcription	Brain Germinal Matrix	brain
27	chr2:47606000-47610400	Genic enhancers	Rectal Mucosa Donor 31	rectum
28	chr2:47606200-47609600	Strong transcription	Fetal Kidney	kidney
29	chr2:47607000-47609800	Strong transcription	Gastric	stomach
30	chr2:47607000-47609800	Strong transcription	Pancreas	Pancrea
31	chr2:47607000-47610600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:47607000-47612400	Strong transcription	Fetal Intestine Small	intestine
33	chr2:47607400-47610200	Strong transcription	Duodenum Mucosa	Duodenum
34	chr2:47607400-47614800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr2:47607800-47615400	Weak transcription	HepG2	liver
36	chr2:47607800-47624000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr2:47608000-47609800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr2:47608000-47609800	Strong transcription	Fetal Stomach	stomach
39	chr2:47608000-47614600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:47608000-47629000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr2:47609200-47609600	Active TSS	Rectal Mucosa Donor 29	rectum
42	chr2:47609200-47611600	Weak transcription	Colonic Mucosa	Colon
43	chr2:47609200-47618200	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr2:47609200-47619600	Strong transcription	Fetal Intestine Large	intestine

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