Variant report

Variant	rs61440530
Chromosome Location	chr12:104527996-104527997
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:104349379..104352032-chr12:104526783..104528784,2	MCF-7	breast:
2	chr12:104510515..104519727-chr12:104525085..104533754,15	MCF-7	breast:
3	chr12:104229182..104230973-chr12:104526385..104528264,2	K562	blood:
4	chr12:104526354..104529452-chr12:104565610..104568678,3	MCF-7	breast:
5	chr12:104487179..104490226-chr12:104527814..104531447,3	K562	blood:

Variant related genes	Relation type
ENSG00000204954	Chromatin interaction
ENSG00000199415	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11837739	0.87[AMR][1000 genomes]
rs17192938	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17193036	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17193064	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17193219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17805891	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17806516	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17806577	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4257050	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59097029	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59714382	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61234792	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61610230	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7313573	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73390481	0.83[ASN][1000 genomes]
rs7979713	1.00[AMR][1000 genomes];0.89[EUR][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	esv1823607	chr12:104506318-104549541	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	n/a
2	esv1816017	chr12:104510676-104531860	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	n/a
3	nsv1045725	chr12:104524153-104614108	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	n/a
4	nsv541586	chr12:104524153-104614108	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104493800-104530600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:104495600-104530800	Weak transcription	Esophagus	oesophagus
3	chr12:104507200-104528000	Strong transcription	Placenta	Placenta
4	chr12:104508000-104528800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:104508200-104529200	Strong transcription	Fetal Thymus	thymus
6	chr12:104508400-104528600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr12:104508600-104529000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:104509000-104528600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr12:104509800-104528600	Weak transcription	Small Intestine	intestine
10	chr12:104510800-104528600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr12:104513800-104528200	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr12:104515600-104529200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:104515800-104528800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr12:104515800-104529200	Strong transcription	Fetal Muscle Trunk	muscle
15	chr12:104516400-104528000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr12:104516600-104528200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr12:104516600-104528800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr12:104519800-104528800	Strong transcription	Primary B cells from cord blood	blood
19	chr12:104520000-104530400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr12:104521000-104528800	Weak transcription	Hela-S3	cervix
21	chr12:104521400-104528600	Strong transcription	Thymus	Thymus
22	chr12:104522600-104528200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr12:104523600-104530600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr12:104523800-104528200	Enhancers	Liver	Liver
25	chr12:104523800-104529800	Weak transcription	Fetal Intestine Small	intestine
26	chr12:104523800-104530400	Enhancers	Fetal Heart	heart
27	chr12:104523800-104530600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr12:104524800-104529000	Strong transcription	Fetal Intestine Large	intestine
29	chr12:104525000-104528600	Strong transcription	Adipose Nuclei	Adipose
30	chr12:104525000-104529000	Strong transcription	Primary T cells from cord blood	blood
31	chr12:104525000-104529000	Enhancers	HSMMtube	muscle
32	chr12:104525200-104528000	Strong transcription	Duodenum Mucosa	Duodenum
33	chr12:104525200-104528400	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr12:104525200-104529000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr12:104525200-104529200	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr12:104525200-104529200	Genic enhancers	HSMM	muscle
37	chr12:104525200-104530400	Weak transcription	Stomach Mucosa	stomach
38	chr12:104525400-104528000	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr12:104525400-104528400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr12:104525400-104528800	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr12:104525400-104528800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr12:104525400-104529600	Genic enhancers	Dnd41	blood
43	chr12:104525600-104528000	Genic enhancers	Duodenum Smooth Muscle	Duodenum
44	chr12:104525600-104529000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr12:104525600-104529000	Genic enhancers	Left Ventricle	heart
46	chr12:104525600-104529000	Genic enhancers	A549	lung
47	chr12:104525600-104530400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr12:104525800-104528600	Weak transcription	Ovary	ovary
49	chr12:104525800-104529000	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr12:104526000-104528200	Strong transcription	Aorta	Aorta

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