Variant report

Variant	rs16866380
Chromosome Location	chr2:179395560-179395561
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:179395497..179400266-chr2:179412543..179417721,4	K562	blood:
2	chr2:179386919..179391089-chr2:179391647..179398872,11	K562	blood:
3	chr2:179386627..179389310-chr2:179394176..179396606,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237298	Chromatin interaction
ENSG00000270277	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10515939	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16866378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16866412	0.84[ASW][hapmap];1.00[GIH][hapmap];0.85[MKK][hapmap];0.82[YRI][hapmap]
rs16866423	1.00[GIH][hapmap]
rs2115558	0.84[ASW][hapmap];1.00[GIH][hapmap];0.85[MKK][hapmap];0.82[YRI][hapmap]
rs2278196	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2288324	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3731744	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3731752	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813243	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3829749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62176135	0.86[EUR][1000 genomes]
rs72646841	0.96[ASN][1000 genomes]
rs72648270	0.95[EUR][1000 genomes];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	nsv834467	chr2:179258140-179430965	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv834468	chr2:179351116-179533625	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS 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

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179388800-179395800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:179388800-179395800	Weak transcription	Placenta	Placenta
3	chr2:179388800-179395800	Weak transcription	Lung	lung
4	chr2:179388800-179396000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:179388800-179396200	Weak transcription	Fetal Kidney	kidney
6	chr2:179388800-179396200	Weak transcription	Gastric	stomach
7	chr2:179388800-179396200	Weak transcription	Pancreas	Pancrea
8	chr2:179388800-179403600	Weak transcription	Esophagus	oesophagus
9	chr2:179388800-179408000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:179388800-179408600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr2:179388800-179410600	Weak transcription	Colonic Mucosa	Colon
12	chr2:179388800-179411800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr2:179388800-179417600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:179388800-179429400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr2:179388800-179441800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr2:179388800-179448800	Weak transcription	Small Intestine	intestine
17	chr2:179388800-179495800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr2:179389000-179395600	Weak transcription	Fetal Intestine Small	intestine
19	chr2:179389000-179395800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr2:179389000-179395800	Weak transcription	Aorta	Aorta
21	chr2:179389000-179396000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr2:179389000-179396000	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr2:179389000-179396000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr2:179389000-179396200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr2:179389000-179396200	Weak transcription	Brain Substantia Nigra	brain
26	chr2:179389000-179396200	Weak transcription	Fetal Brain Female	brain
27	chr2:179389200-179396200	Weak transcription	Brain Anterior Caudate	brain
28	chr2:179389200-179396200	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr2:179389200-179412600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr2:179389400-179395600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr2:179389400-179395600	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr2:179389400-179395600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr2:179389400-179395600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr2:179389400-179395600	Weak transcription	Right Atrium	heart
35	chr2:179389400-179395800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr2:179389400-179396000	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr2:179389400-179396000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:179389400-179396000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr2:179389400-179396000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:179389400-179396000	Weak transcription	Brain Angular Gyrus	brain
41	chr2:179389400-179396000	Weak transcription	Fetal Lung	lung
42	chr2:179389400-179396000	Weak transcription	Ovary	ovary
43	chr2:179389400-179396000	Weak transcription	Stomach Smooth Muscle	stomach
44	chr2:179389400-179396000	Weak transcription	A549	lung
45	chr2:179389400-179396200	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr2:179389400-179396200	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr2:179389400-179396200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr2:179389400-179396200	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr2:179389400-179396200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr2:179389400-179396200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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