Variant report

Variant	rs3812802
Chromosome Location	chr12:104215874-104215875
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104211016..104214804-chr12:104214822..104218776,4	K562	blood:
2	chr12:104211319..104217420-chr12:104233507..104236073,8	MCF-7	breast:
3	chr12:104214519..104222192-chr12:104231005..104236989,8	K562	blood:
4	chr12:104213748..104215908-chr12:104239137..104241310,2	K562	blood:
5	chr12:104215538..104217746-chr12:104226059..104228038,3	K562	blood:

Variant related genes	Relation type
ENSG00000257327	Chromatin interaction
ENSG00000257754	Chromatin interaction
ENSG00000111696	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs12422418	0.92[EUR][1000 genomes]
rs12422615	0.88[EUR][1000 genomes]
rs12422701	0.89[EUR][1000 genomes]
rs12423476	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12423889	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12423912	0.93[EUR][1000 genomes]
rs12423994	0.90[EUR][1000 genomes]
rs12424929	0.89[EUR][1000 genomes]
rs12424984	0.85[EUR][1000 genomes]
rs12425283	0.93[EUR][1000 genomes]
rs1437505	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1550207	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1550208	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17034593	0.90[EUR][1000 genomes]
rs17034620	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17034625	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17034637	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17034639	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17034640	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17034642	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17034645	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17034648	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17034650	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17034662	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17794246	0.89[EUR][1000 genomes]
rs2289258	0.89[EUR][1000 genomes]
rs3751196	0.84[EUR][1000 genomes]
rs55736751	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55810720	0.90[EUR][1000 genomes]
rs55932227	0.89[EUR][1000 genomes]
rs55949441	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55987022	0.89[EUR][1000 genomes]
rs55993375	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56123042	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56143748	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56147174	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56255894	0.85[EUR][1000 genomes]
rs56314567	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56403068	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57173983	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59651914	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59716163	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs60378307	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61512578	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61748068	0.90[EUR][1000 genomes]
rs7135803	0.88[AFR][1000 genomes]
rs7295408	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7314150	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7485127	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899482	chr12:104092996-104218956	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv34031	chr12:104114277-104298546	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv899483	chr12:104117462-104218956	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv899487	chr12:104118587-104218956	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv899489	chr12:104144835-104218956	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv899490	chr12:104149022-104218956	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104171800-104216000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr12:104193000-104217600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:104196400-104221800	Weak transcription	Brain Anterior Caudate	brain
4	chr12:104200200-104216200	Weak transcription	NHDF-Ad	bronchial
5	chr12:104202200-104218200	Weak transcription	Gastric	stomach
6	chr12:104207400-104217200	Weak transcription	Fetal Intestine Large	intestine
7	chr12:104208200-104221800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr12:104208200-104223200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr12:104208200-104227800	Weak transcription	Pancreas	Pancrea
10	chr12:104208600-104221200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:104208800-104227600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:104212000-104218200	Enhancers	Colon Smooth Muscle	Colon
13	chr12:104213400-104217600	Weak transcription	Psoas Muscle	Psoas
14	chr12:104213600-104218000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr12:104213800-104218800	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr12:104214600-104216000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr12:104214600-104216000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:104214600-104216400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr12:104214800-104216400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr12:104214800-104219400	Weak transcription	Ovary	ovary
21	chr12:104215000-104216000	Genic enhancers	HSMM	muscle
22	chr12:104215000-104216600	Enhancers	NH-A	brain
23	chr12:104215000-104219800	Enhancers	Muscle Satellite Cultured Cells	--
24	chr12:104215200-104216200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr12:104215200-104217800	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr12:104215200-104218600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr12:104215200-104218800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:104215200-104221800	Weak transcription	Aorta	Aorta
29	chr12:104215200-104226000	Weak transcription	Primary hematopoietic stem cells	blood
30	chr12:104215200-104227600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr12:104215400-104216200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr12:104215400-104216600	Strong transcription	K562	blood
33	chr12:104215400-104216800	Enhancers	Osteobl	bone
34	chr12:104215400-104217000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr12:104215400-104217600	Weak transcription	Fetal Muscle Leg	muscle
36	chr12:104215400-104218600	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr12:104215400-104221200	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr12:104215400-104221600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr12:104215400-104221600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr12:104215400-104221600	Weak transcription	HepG2	liver
41	chr12:104215400-104221800	Weak transcription	Brain Angular Gyrus	brain
42	chr12:104215400-104223400	Enhancers	Rectal Smooth Muscle	rectum
43	chr12:104215600-104216600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr12:104215600-104216600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr12:104215600-104216600	Enhancers	HMEC	breast
46	chr12:104215600-104216600	Enhancers	NHEK	skin
47	chr12:104215800-104216000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr12:104215800-104217200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr12:104215800-104218400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr12:104215800-104218400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links