Variant report

Variant	rs10849790
Chromosome Location	chr12:121232328-121232329
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	chr12:121227665..121229362-chr12:121229925..121232592,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs1027556	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1039302	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10431387	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10437838	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10744754	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10774568	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10774569	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10774571	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10849782	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10849783	0.81[EUR][1000 genomes]
rs10849786	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10849787	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10849788	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10849793	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10849794	0.84[EUR][1000 genomes]
rs10849800	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11065259	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11065266	0.96[EUR][1000 genomes]
rs11065272	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs11833706	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12423697	0.84[EUR][1000 genomes]
rs2393718	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2393725	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3213568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3213569	0.96[EUR][1000 genomes]
rs3213571	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4638383	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs56137011	0.84[EUR][1000 genomes]
rs593429	0.83[ASN][1000 genomes]
rs6489780	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6489781	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6489782	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6490303	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7135147	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7135426	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs715319	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7300695	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73229114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7960784	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7965332	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7977343	0.87[AMR][1000 genomes];0.83[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	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv560438	chr12:121194565-121352206	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv1801139	chr12:121228410-121241933	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1045178	chr12:121231461-121271734	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121206200-121238600	Weak transcription	Small Intestine	intestine
2	chr12:121207200-121233000	Weak transcription	HSMMtube	muscle
3	chr12:121209400-121236800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr12:121211400-121260800	Weak transcription	Gastric	stomach
5	chr12:121212600-121236600	Weak transcription	Fetal Heart	heart
6	chr12:121221000-121250000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr12:121221200-121233000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr12:121221200-121233600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr12:121221200-121249400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr12:121221400-121232800	Weak transcription	A549	lung
11	chr12:121221400-121235800	Weak transcription	Hela-S3	cervix
12	chr12:121221400-121240800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr12:121221600-121238800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr12:121222000-121233200	Weak transcription	NHEK	skin
15	chr12:121222000-121233800	Weak transcription	Fetal Stomach	stomach
16	chr12:121222200-121237200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:121222200-121274000	Weak transcription	Lung	lung
18	chr12:121222400-121238800	Weak transcription	Placenta	Placenta
19	chr12:121222400-121240400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr12:121222600-121233200	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr12:121222600-121237200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr12:121222600-121249200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr12:121222600-121259000	Weak transcription	Ovary	ovary
24	chr12:121222600-121260800	Weak transcription	Spleen	Spleen
25	chr12:121222600-121268600	Weak transcription	Esophagus	oesophagus
26	chr12:121222600-121268600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr12:121222800-121233200	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr12:121222800-121237200	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr12:121222800-121237400	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr12:121222800-121240600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr12:121222800-121245600	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr12:121222800-121249400	Weak transcription	HSMM	muscle
33	chr12:121223000-121233000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr12:121226200-121237200	Weak transcription	Psoas Muscle	Psoas
35	chr12:121226400-121232600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr12:121227000-121232600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr12:121228600-121232400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr12:121228600-121232800	Weak transcription	Dnd41	blood
39	chr12:121228600-121233200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr12:121228600-121233800	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr12:121228600-121233800	Weak transcription	Fetal Thymus	thymus
42	chr12:121228600-121235600	Weak transcription	Thymus	Thymus
43	chr12:121228600-121239400	Weak transcription	Liver	Liver
44	chr12:121228800-121233800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr12:121229000-121232800	Weak transcription	Primary B cells from cord blood	blood
46	chr12:121229000-121245200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr12:121230000-121232600	Weak transcription	Fetal Lung	lung
48	chr12:121230000-121239000	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr12:121230000-121255200	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr12:121230600-121236000	Weak transcription	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links