Variant report

Variant	rs16949828
Chromosome Location	chr12:120429476-120429477
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:120419275..120421989-chr12:120429002..120431271,2	K562	blood:
2	chr12:120427745..120429727-chr12:120729725..120731576,2	MCF-7	breast:
3	chr12:120427086..120431307-chr12:120435070..120439124,5	MCF-7	breast:
4	chr12:120428276..120430346-chr12:120637372..120639264,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135127	Chromatin interaction
ENSG00000255857	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000089157	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10492050	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12301083	1.00[EUR][1000 genomes]
rs16949884	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16949890	1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16949897	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs35938105	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3852590	1.00[EUR][1000 genomes]
rs61733796	1.00[EUR][1000 genomes]
rs7953006	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv510575	chr12:120303163-120437490	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv3525916	chr12:120345352-120665045	Bivalent Enhancer Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
3	esv3525917	chr12:120345352-120665045	Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
4	nsv899554	chr12:120389613-120513625	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	esv1844134	chr12:120426469-120441443	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv1845761	chr12:120426469-120441443	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv1797666	chr12:120426666-120449259	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	esv1807589	chr12:120426666-120449259	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120427800-120431000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
2	chr12:120428000-120429600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
3	chr12:120428000-120432200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
4	chr12:120428400-120435600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:120428600-120429600	Bivalent Enhancer	Fetal Brain Male	brain
6	chr12:120428600-120430600	Enhancers	HepG2	liver
7	chr12:120428600-120445000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:120428600-120449800	Weak transcription	Brain Anterior Caudate	brain
9	chr12:120428600-120453200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr12:120428800-120429600	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr12:120428800-120430200	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr12:120428800-120431800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr12:120428800-120432400	Weak transcription	Primary B cells from peripheral blood	blood
14	chr12:120428800-120433200	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr12:120428800-120435800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr12:120428800-120444000	Weak transcription	NHEK	skin
17	chr12:120428800-120444200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr12:120428800-120447800	Weak transcription	Gastric	stomach
19	chr12:120428800-120451400	Weak transcription	HMEC	breast
20	chr12:120428800-120451600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr12:120429000-120429800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr12:120429000-120430400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr12:120429000-120431400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr12:120429000-120436200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr12:120429000-120440600	Weak transcription	Fetal Brain Female	brain
26	chr12:120429000-120443800	Weak transcription	Hela-S3	cervix
27	chr12:120429000-120450000	Weak transcription	Esophagus	oesophagus
28	chr12:120429200-120430000	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr12:120429200-120436200	Weak transcription	Fetal Thymus	thymus
30	chr12:120429400-120430000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr12:120429400-120430200	Enhancers	Primary T cells from cord blood	blood
32	chr12:120429400-120430200	Weak transcription	Thymus	Thymus
33	chr12:120429400-120432600	Weak transcription	GM12878-XiMat	blood
34	chr12:120429400-120432800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr12:120429400-120436200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:120429400-120443200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr12:120429400-120445200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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