Variant report

Variant	rs880797
Chromosome Location	chr12:105621155-105621156
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:105501403..105502983-chr12:105619326..105621354,2	MCF-7	breast:
2	chr12:105608225..105613366-chr12:105619333..105624104,5	MCF-7	breast:
3	chr12:105620755..105625323-chr12:105625745..105629848,5	K562	blood:
4	chr12:105499627..105501658-chr12:105620143..105622423,2	K562	blood:
5	chr12:105616267..105619374-chr12:105619746..105623496,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136044	Chromatin interaction
ENSG00000136051	Chromatin interaction
ENSG00000257999	Chromatin interaction
ENSG00000235162	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1107756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1109433	0.98[ASN][1000 genomes]
rs11112416	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1196751	0.95[CHB][hapmap];0.80[ASN][1000 genomes]
rs1196758	0.95[CHB][hapmap]
rs1196761	0.81[CHB][hapmap]
rs1196769	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1196771	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1196773	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196794	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1196830	0.90[EUR][1000 genomes]
rs1196845	0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[EUR][1000 genomes]
rs1211627	0.90[EUR][1000 genomes]
rs12815031	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.98[ASN][1000 genomes]
rs1317955	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1470381	0.98[ASN][1000 genomes]
rs2246510	0.95[CHB][hapmap]
rs2293644	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2440695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2440706	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2464184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3794222	0.98[ASN][1000 genomes]
rs3794223	0.81[CHB][hapmap]
rs3829296	0.98[ASN][1000 genomes]
rs752471	0.81[CHB][hapmap]
rs881279	0.95[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	nsv832506	chr12:105461274-105637561	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv455704	chr12:105583877-105651356	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
3	nsv560053	chr12:105583877-105651356	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
4	nsv899499	chr12:105616297-105722529	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105546800-105625200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:105578000-105623200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr12:105584000-105627000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr12:105596400-105621800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:105600800-105626800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:105605600-105628400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr12:105609200-105622400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:105609200-105626800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:105609200-105628600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr12:105611200-105621200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr12:105611200-105628200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr12:105611400-105621200	Weak transcription	Hela-S3	cervix
13	chr12:105611600-105621200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr12:105611600-105621600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr12:105611600-105626200	Weak transcription	Fetal Brain Male	brain
16	chr12:105611800-105621200	Weak transcription	Fetal Kidney	kidney
17	chr12:105612000-105624800	Genic enhancers	NHDF-Ad	bronchial
18	chr12:105612800-105624200	Strong transcription	Fetal Stomach	stomach
19	chr12:105613000-105623600	Strong transcription	Fetal Muscle Trunk	muscle
20	chr12:105613800-105622000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:105616000-105621200	Weak transcription	HMEC	breast
22	chr12:105616400-105623200	Strong transcription	Fetal Brain Female	brain
23	chr12:105616600-105629000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr12:105617000-105621200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr12:105617000-105621200	Weak transcription	Fetal Lung	lung
26	chr12:105617000-105623200	Strong transcription	Stomach Smooth Muscle	stomach
27	chr12:105617000-105629000	Weak transcription	Esophagus	oesophagus
28	chr12:105617200-105621200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr12:105617400-105622800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr12:105617400-105625400	Genic enhancers	Muscle Satellite Cultured Cells	--
31	chr12:105617400-105629000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr12:105617600-105625400	Strong transcription	A549	lung
33	chr12:105618000-105621200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr12:105618000-105621200	Weak transcription	Brain Germinal Matrix	brain
35	chr12:105618000-105621200	Weak transcription	Lung	lung
36	chr12:105618200-105621200	Enhancers	Brain Hippocampus Middle	brain
37	chr12:105618200-105625200	Weak transcription	Right Ventricle	heart
38	chr12:105618400-105621200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr12:105618600-105621200	Weak transcription	Colonic Mucosa	Colon
40	chr12:105618600-105625200	Weak transcription	Spleen	Spleen
41	chr12:105618600-105626800	Weak transcription	Gastric	stomach
42	chr12:105619200-105623000	Strong transcription	Placenta	Placenta
43	chr12:105619400-105625200	Genic enhancers	HSMM	muscle
44	chr12:105619400-105627400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:105619800-105622600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:105620000-105621400	Genic enhancers	Brain Inferior Temporal Lobe	brain
47	chr12:105620000-105621400	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr12:105620000-105621800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr12:105620000-105622000	Strong transcription	Fetal Intestine Large	intestine
50	chr12:105620000-105622400	Strong transcription	HUES6 Cell Line	embryonic stem cell

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