Variant report

Variant	rs1896563
Chromosome Location	chr12:105007640-105007641
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:104995437..104998034-chr12:105002964..105009191,6	K562	blood:
2	chr12:104995437..104998034-chr12:105005195..105009191,4	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10507177	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778343	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs10778346	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10861255	0.95[EUR][1000 genomes]
rs10861256	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10861261	1.00[CHB][hapmap]
rs11112132	0.98[ASN][1000 genomes]
rs11112136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112143	1.00[CHB][hapmap]
rs1541795	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17815142	1.00[CHB][hapmap]
rs4964826	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7133744	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7304590	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs875679	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832504	chr12:104853331-105028245	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers 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	9 gene(s)	inside rSNPs	diseases
2	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1050695	chr12:105000981-105125161	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv541589	chr12:105000981-105125161	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104989400-105030600	Strong transcription	Dnd41	blood
2	chr12:104993200-105012600	Weak transcription	Gastric	stomach
3	chr12:104998000-105008600	Weak transcription	Right Ventricle	heart
4	chr12:104998200-105008400	Weak transcription	Esophagus	oesophagus
5	chr12:104998400-105008400	Weak transcription	Aorta	Aorta
6	chr12:104998400-105008400	Weak transcription	Right Atrium	heart
7	chr12:104998400-105008600	Weak transcription	Small Intestine	intestine
8	chr12:104998600-105008600	Weak transcription	Primary T cells from cord blood	blood
9	chr12:104998600-105012800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:104998800-105031400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr12:104999000-105026800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr12:104999800-105008800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr12:104999800-105012800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr12:105000000-105020400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr12:105000000-105021000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:105000200-105008400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr12:105000400-105008400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr12:105000400-105008400	Weak transcription	Adipose Nuclei	Adipose
19	chr12:105000400-105009200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:105000400-105014600	Weak transcription	Osteobl	bone
21	chr12:105000400-105014800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr12:105000400-105019800	Weak transcription	HMEC	breast
23	chr12:105000400-105026000	Weak transcription	NHLF	lung
24	chr12:105000600-105012800	Weak transcription	Lung	lung
25	chr12:105000800-105008600	Weak transcription	HSMMtube	muscle
26	chr12:105002800-105013800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr12:105003200-105014200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr12:105003400-105008800	Weak transcription	Brain Anterior Caudate	brain
29	chr12:105003600-105014600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr12:105003600-105020200	Weak transcription	NHEK	skin
31	chr12:105004600-105008200	Weak transcription	Placenta	Placenta
32	chr12:105004600-105015000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr12:105004800-105013200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:105005400-105008000	Weak transcription	Fetal Stomach	stomach
35	chr12:105005800-105019800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:105006000-105012400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr12:105006000-105014800	Weak transcription	Spleen	Spleen
38	chr12:105006000-105016400	Weak transcription	A549	lung
39	chr12:105006000-105028200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr12:105006200-105012600	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr12:105006200-105012800	Weak transcription	Fetal Thymus	thymus
42	chr12:105006200-105034800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr12:105006400-105014000	Weak transcription	Brain Hippocampus Middle	brain
44	chr12:105006600-105007800	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr12:105006600-105012400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr12:105006600-105022600	Weak transcription	Primary B cells from cord blood	blood
47	chr12:105006800-105008400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr12:105006800-105008400	Weak transcription	Fetal Heart	heart
49	chr12:105006800-105008600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr12:105006800-105009400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links