Variant report

Variant	rs6487268
Chromosome Location	chr12:22210380-22210381
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:22198261..22201239-chr12:22208109..22210711,2	K562	blood:
2	chr12:22207097..22209005-chr12:22210262..22212255,2	K562	blood:
3	chr12:22198387..22201385-chr12:22209134..22211301,2	K562	blood:
4	chr12:22199607..22203065-chr12:22209223..22212376,4	MCF-7	breast:
5	chr12:22208985..22211876-chr12:22213406..22216314,4	K562	blood:

Variant related genes	Relation type
ENSG00000111726	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10841928	0.80[AMR][1000 genomes]
rs10841929	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10841931	0.95[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10841932	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10841933	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10841934	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10841935	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10841936	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11046275	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11046276	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11046281	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11046289	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11046290	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11046291	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11046292	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11046297	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2058849	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2111352	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2216296	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2418037	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2418038	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2955515	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2970800	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3809204	0.93[ASN][1000 genomes]
rs6487272	0.96[CEU][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6487273	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6487275	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6487276	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7135019	0.96[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs731355	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7316741	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7316854	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs759582	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[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	nsv1051073	chr12:21910875-22271209	Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv2758298	chr12:22140834-22339299	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv2759883	chr12:22140834-22736907	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv438196	chr12:22195202-22234058	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv1850259	chr12:22198865-22244741	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:22200000-22214400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:22200000-22218200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:22200000-22220200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:22200000-22220200	Weak transcription	Lung	lung
5	chr12:22200200-22215200	Weak transcription	HSMMtube	muscle
6	chr12:22200200-22215800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr12:22200200-22219600	Weak transcription	Aorta	Aorta
8	chr12:22200400-22216600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:22200400-22220400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr12:22200800-22210800	Weak transcription	Fetal Stomach	stomach
11	chr12:22200800-22220800	Weak transcription	Fetal Heart	heart
12	chr12:22201200-22211400	Weak transcription	Hela-S3	cervix
13	chr12:22201400-22220400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr12:22201800-22219000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr12:22202000-22218000	Weak transcription	Psoas Muscle	Psoas
16	chr12:22202000-22219600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr12:22202000-22220200	Weak transcription	Fetal Brain Male	brain
18	chr12:22202200-22217000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr12:22202200-22218000	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr12:22202200-22223800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr12:22203800-22220200	Weak transcription	Esophagus	oesophagus
22	chr12:22203800-22220200	Weak transcription	Small Intestine	intestine
23	chr12:22203800-22235200	Weak transcription	Gastric	stomach
24	chr12:22204000-22215400	Weak transcription	Brain Angular Gyrus	brain
25	chr12:22204400-22215400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr12:22204600-22219400	Weak transcription	Stomach Mucosa	stomach
27	chr12:22204600-22223400	Weak transcription	Pancreas	Pancrea
28	chr12:22205200-22222200	Weak transcription	Fetal Intestine Small	intestine
29	chr12:22207000-22218400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:22207000-22220200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr12:22207400-22210400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr12:22207600-22218800	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr12:22207600-22219400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr12:22207800-22219000	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr12:22208000-22210400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr12:22208000-22210400	Strong transcription	Colon Smooth Muscle	Colon
37	chr12:22208000-22210600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:22208000-22212400	Strong transcription	HMEC	breast
39	chr12:22208000-22212600	Strong transcription	Placenta	Placenta
40	chr12:22208000-22219600	Strong transcription	Duodenum Mucosa	Duodenum
41	chr12:22208000-22219800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr12:22208000-22219800	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr12:22208200-22210400	Strong transcription	Adipose Nuclei	Adipose
44	chr12:22208200-22212800	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr12:22208200-22216800	Strong transcription	Primary B cells from peripheral blood	blood
46	chr12:22208200-22217000	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr12:22208400-22210400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr12:22208400-22210400	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr12:22208400-22210400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr12:22208400-22210400	Strong transcription	Dnd41	blood

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