Variant report

Variant	rs12080452
Chromosome Location	chr1:227378649-227378650
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227373675..227376391-chr1:227377073..227380557,3	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10458379	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10799411	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10916098	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10916110	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10916117	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs12033050	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12035190	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12035998	0.81[CEU][hapmap];1.00[CHB][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12038272	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs12073573	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12079122	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12079173	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12095674	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12097121	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1929859	0.81[ASN][1000 genomes]
rs2458523	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2482453	0.81[ASN][1000 genomes]
rs2997438	0.82[JPT][hapmap]
rs4065211	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4551562	0.83[AMR][1000 genomes]
rs4653788	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4653790	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs477373	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs482032	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs533134	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs567467	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58442036	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs595155	0.80[AMR][1000 genomes]
rs61700597	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61834563	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61834564	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61836477	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs645081	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6660043	0.83[EUR][1000 genomes]
rs6664803	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6699534	0.86[EUR][1000 genomes]
rs688718	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72757311	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7513122	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7536444	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs871210	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][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	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer 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	35 gene(s)	inside rSNPs	diseases
3	esv2830098	chr1:227295716-227422234	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
5	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227288400-227398000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:227300000-227379800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:227329600-227380000	Weak transcription	Aorta	Aorta
4	chr1:227333400-227381000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr1:227333400-227405600	Weak transcription	Adipose Nuclei	Adipose
6	chr1:227343200-227400400	Weak transcription	A549	lung
7	chr1:227346800-227379800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:227346800-227403800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr1:227346800-227405800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr1:227346800-227406800	Weak transcription	Fetal Kidney	kidney
11	chr1:227347800-227385800	Weak transcription	Fetal Intestine Small	intestine
12	chr1:227347800-227390400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:227348200-227379800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:227348200-227398000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:227348200-227398400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr1:227348200-227401600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr1:227348200-227408400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr1:227348200-227412200	Weak transcription	Fetal Muscle Leg	muscle
19	chr1:227355400-227379800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr1:227355400-227386200	Weak transcription	Brain Anterior Caudate	brain
21	chr1:227359200-227379600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:227359400-227379800	Weak transcription	Brain Angular Gyrus	brain
23	chr1:227359400-227379800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:227359400-227379800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr1:227359400-227389000	Weak transcription	Right Ventricle	heart
26	chr1:227360800-227401200	Weak transcription	Hela-S3	cervix
27	chr1:227362800-227379800	Weak transcription	NHLF	lung
28	chr1:227363000-227379600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr1:227363800-227380600	Weak transcription	Esophagus	oesophagus
30	chr1:227364000-227379800	Weak transcription	HSMMtube	muscle
31	chr1:227364000-227385800	Weak transcription	Fetal Stomach	stomach
32	chr1:227364200-227381000	Weak transcription	Duodenum Mucosa	Duodenum
33	chr1:227365800-227399400	Weak transcription	Fetal Intestine Large	intestine
34	chr1:227369000-227379600	Weak transcription	HMEC	breast
35	chr1:227369200-227382600	Weak transcription	Fetal Brain Female	brain
36	chr1:227370000-227413600	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr1:227370600-227379400	Weak transcription	NHDF-Ad	bronchial
38	chr1:227370600-227380000	Weak transcription	Gastric	stomach
39	chr1:227371400-227381000	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr1:227371600-227380000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:227371600-227381600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr1:227371800-227379400	Weak transcription	HSMM	muscle
43	chr1:227371800-227380000	Weak transcription	Lung	lung
44	chr1:227372200-227379800	Weak transcription	NHEK	skin
45	chr1:227372600-227379800	Weak transcription	K562	blood
46	chr1:227373400-227379800	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr1:227373400-227397800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr1:227374400-227401600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr1:227374600-227401600	Weak transcription	Left Ventricle	heart
50	chr1:227374800-227391000	Weak transcription	Brain Hippocampus Middle	brain

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