Variant report

Variant	rs12628475
Chromosome Location	chr22:29606907-29606908
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr22:29606718-29607019	GM12878	blood:	n/a	n/a
2	POLR2A	chr22:29606806-29607883	GM12892	blood:	n/a	n/a
3	POLR2A	chr22:29606828-29607731	GM12878	blood:	n/a	n/a
4	NR2C2	chr22:29606906-29607719	GM12878	blood:	n/a	n/a
5	POLR2A	chr22:29606693-29607824	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr22:29601902..29603639-chr22:29605724..29608269,2	K562	blood:
2	chr22:29605515..29607665-chr22:29648338..29651149,2	K562	blood:
3	chr22:29601072..29604199-chr22:29606005..29610482,4	MCF-7	breast:

Variant related genes	Relation type
EMID1	TF binding region
ENSG00000186998	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10427585	0.84[EUR][1000 genomes]
rs11090561	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12484227	0.92[AFR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12484888	0.92[AFR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12484912	0.92[AFR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12484942	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12627935	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12628053	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12628113	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12628212	0.92[AFR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12628310	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16987237	0.92[AFR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2301446	1.00[CEU][hapmap]
rs35405773	0.88[AFR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4823018	1.00[CEU][hapmap]
rs55676901	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56132535	0.92[AFR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59125412	0.84[AFR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60307207	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61041761	0.82[EUR][1000 genomes]
rs67133001	0.91[ASN][1000 genomes]
rs73399031	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73882489	0.88[AFR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73882490	0.88[AFR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73882499	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8138012	0.94[ASN][1000 genomes]
rs8141926	0.94[ASN][1000 genomes]
rs8142082	0.94[ASN][1000 genomes]
rs8142429	0.94[ASN][1000 genomes]
rs916341	1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs916342	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[EUR][1000 genomes];0.94[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	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv524483	chr22:29525126-29630337	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv914958	chr22:29586058-29620599	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv1809952	chr22:29595349-29661434	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	esv1806500	chr22:29604787-29635071	Enhancers Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29602800-29611000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr22:29602800-29616000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr22:29602800-29616000	Weak transcription	Ovary	ovary
4	chr22:29603000-29610800	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr22:29603400-29608800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr22:29603400-29611000	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr22:29603800-29612600	Weak transcription	Brain Angular Gyrus	brain
8	chr22:29604000-29616200	Weak transcription	Thymus	Thymus
9	chr22:29604600-29608400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr22:29604800-29612600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr22:29605000-29607000	Enhancers	H1 Cell Line	embryonic stem cell
12	chr22:29605000-29607200	Enhancers	Fetal Brain Male	brain
13	chr22:29605000-29619400	Weak transcription	Colonic Mucosa	Colon
14	chr22:29605400-29607000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr22:29605400-29607800	Genic enhancers	Spleen	Spleen
16	chr22:29605400-29612200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr22:29605400-29612600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr22:29605400-29614400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr22:29605400-29616000	Weak transcription	Lung	lung
20	chr22:29605600-29607200	Weak transcription	Duodenum Mucosa	Duodenum
21	chr22:29605600-29607200	Weak transcription	Fetal Heart	heart
22	chr22:29605600-29607200	Weak transcription	Gastric	stomach
23	chr22:29605800-29607600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr22:29605800-29609000	Strong transcription	Fetal Stomach	stomach
25	chr22:29605800-29611200	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr22:29605800-29611400	Weak transcription	Brain Germinal Matrix	brain
27	chr22:29605800-29612400	Weak transcription	Brain Anterior Caudate	brain
28	chr22:29605800-29612800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr22:29606000-29607600	Genic enhancers	Fetal Intestine Small	intestine
30	chr22:29606000-29609000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr22:29606000-29611800	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr22:29606000-29612600	Weak transcription	Brain Hippocampus Middle	brain
33	chr22:29606200-29608400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr22:29606200-29610200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr22:29606200-29611000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr22:29606200-29611800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr22:29606200-29616000	Strong transcription	Fetal Intestine Large	intestine
38	chr22:29606600-29607400	Flanking Active TSS	Fetal Brain Female	brain
39	chr22:29606600-29607800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr22:29606800-29607000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr22:29606800-29607000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
42	chr22:29606800-29607000	Active TSS	GM12878-XiMat	blood
43	chr22:29606800-29607200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr22:29606800-29607400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr22:29606800-29607400	Transcr. at gene 5' and 3'	Dnd41	blood
46	chr22:29606800-29607600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr22:29606800-29607600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr22:29606800-29607600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr22:29606800-29607600	Transcr. at gene 5' and 3'	Fetal Kidney	kidney
50	chr22:29606800-29607800	Strong transcription	Primary hematopoietic stem cells	blood

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