Variant report

Variant	rs3829749
Chromosome Location	chr2:179395760-179395761
allele	C/T
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: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10497518	0.89[ASW][hapmap];0.91[LWK][hapmap];0.90[YRI][hapmap]
rs10515939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[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]
rs16866378	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16866380	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	1.00[GIH][hapmap]
rs16866423	1.00[GIH][hapmap]
rs2115558	1.00[GIH][hapmap]
rs2278196	1.00[CEU][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2288324	0.90[ASW][hapmap];1.00[CEU][hapmap];0.88[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3731744	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3731752	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]
rs3813243	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[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:3 , 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
3	nsv522036	chr2:179395760-179398509	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 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	chr2:179389000-179395800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:179389000-179395800	Weak transcription	Aorta	Aorta
20	chr2:179389000-179396000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr2:179389000-179396000	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr2:179389000-179396000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr2:179389000-179396200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr2:179389000-179396200	Weak transcription	Brain Substantia Nigra	brain
25	chr2:179389000-179396200	Weak transcription	Fetal Brain Female	brain
26	chr2:179389200-179396200	Weak transcription	Brain Anterior Caudate	brain
27	chr2:179389200-179396200	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr2:179389200-179412600	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr2:179389400-179395800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr2:179389400-179396000	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr2:179389400-179396000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:179389400-179396000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr2:179389400-179396000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr2:179389400-179396000	Weak transcription	Brain Angular Gyrus	brain
35	chr2:179389400-179396000	Weak transcription	Fetal Lung	lung
36	chr2:179389400-179396000	Weak transcription	Ovary	ovary
37	chr2:179389400-179396000	Weak transcription	Stomach Smooth Muscle	stomach
38	chr2:179389400-179396000	Weak transcription	A549	lung
39	chr2:179389400-179396200	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr2:179389400-179396200	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr2:179389400-179396200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr2:179389400-179396200	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr2:179389400-179396200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr2:179389400-179396200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr2:179389400-179396200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr2:179389400-179396200	Weak transcription	Liver	Liver
47	chr2:179389400-179396200	Weak transcription	Brain Cingulate Gyrus	brain
48	chr2:179389400-179396200	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr2:179389400-179396200	Weak transcription	Colon Smooth Muscle	Colon
50	chr2:179389400-179396200	Weak transcription	Duodenum Mucosa	Duodenum

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