Variant report

Variant	rs12216122
Chromosome Location	chr6:143161092-143161093
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	EBF1	chr6:143160267-143161318	GM12878	blood:	n/a	n/a
2	EP300	chr6:143160597-143161122	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:143160527-143161426	GM12878	blood:	n/a	n/a
4	POLR2A	chr6:143160622-143161144	GM12878	blood:	n/a	n/a
5	RUNX3	chr6:143159919-143161383	GM12878	blood:	n/a	chr6:143161212-143161229 chr6:143160303-143160312 chr6:143160303-143160312
6	WRNIP1	chr6:143160774-143161318	GM12878	blood:	n/a	n/a
7	CTCF	chr6:143160738-143161254	GM12878	blood:	n/a	n/a
8	CEBPB	chr6:143160666-143161156	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:143161057..143162645-chr6:143163973..143165505,2	K562	blood:
2	chr6:143160497..143162652-chr6:143164958..143167111,2	MCF-7	breast:
3	chr6:143153290..143155432-chr6:143159116..143161535,2	MCF-7	breast:
4	chr6:143160531..143162913-chr6:143266155..143268923,2	MCF-7	breast:

Variant related genes	Relation type
HIVEP2	TF binding region
ENSG00000010818	Chromatin interaction

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

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

rs_ID	r²[population]
rs10457743	0.81[AFR][1000 genomes]
rs12190352	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12194370	1.00[AFR][1000 genomes]
rs12194419	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12197240	1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12203103	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap];1.00[AFR][1000 genomes]
rs1334487	0.82[AFR][1000 genomes]
rs199240	1.00[JPT][hapmap]
rs200143	1.00[JPT][hapmap]
rs200145	1.00[JPT][hapmap]
rs200148	1.00[JPT][hapmap]
rs55795539	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55994331	0.81[AFR][1000 genomes]
rs62430706	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62430708	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs763535	0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830829	chr6:143058408-143218077	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143144000-143165800	Weak transcription	Liver	Liver
2	chr6:143144600-143163000	Weak transcription	Dnd41	blood
3	chr6:143144600-143163200	Weak transcription	Fetal Thymus	thymus
4	chr6:143144800-143162400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr6:143144800-143163000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:143144800-143166800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:143149200-143166000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr6:143149400-143163200	Weak transcription	Adipose Nuclei	Adipose
9	chr6:143149400-143163600	Weak transcription	Fetal Lung	lung
10	chr6:143149600-143165600	Weak transcription	Colon Smooth Muscle	Colon
11	chr6:143151400-143163200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr6:143152000-143163400	Weak transcription	Thymus	Thymus
13	chr6:143152600-143163000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr6:143152800-143163600	Weak transcription	Fetal Stomach	stomach
15	chr6:143154600-143163000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr6:143154600-143163600	Weak transcription	Aorta	Aorta
17	chr6:143155000-143162600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:143155400-143162800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr6:143155400-143162800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:143155800-143163400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr6:143157000-143163000	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr6:143157000-143163200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr6:143157200-143163000	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr6:143157600-143163600	Weak transcription	Brain Angular Gyrus	brain
25	chr6:143157600-143163600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr6:143157600-143164600	Weak transcription	Fetal Brain Female	brain
27	chr6:143158000-143161400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr6:143158000-143163000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr6:143158000-143163600	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr6:143158400-143163000	Weak transcription	Fetal Brain Male	brain
31	chr6:143158600-143163000	Enhancers	Primary T cells from cord blood	blood
32	chr6:143158800-143161400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr6:143159000-143161200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:143159000-143163200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr6:143159200-143161200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:143159200-143161400	Enhancers	Hela-S3	cervix
37	chr6:143159400-143161400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr6:143159600-143161200	Enhancers	Primary B cells from cord blood	blood
39	chr6:143159600-143161400	Enhancers	Small Intestine	intestine
40	chr6:143159600-143161400	Enhancers	Stomach Mucosa	stomach
41	chr6:143159800-143161200	Enhancers	NH-A	brain
42	chr6:143159800-143161400	Enhancers	Primary B cells from peripheral blood	blood
43	chr6:143159800-143161400	Enhancers	HUVEC	blood vessel
44	chr6:143159800-143161400	Enhancers	Osteobl	bone
45	chr6:143160000-143161200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr6:143160000-143161400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr6:143160000-143161400	Flanking Active TSS	GM12878-XiMat	blood
48	chr6:143160000-143161400	Enhancers	NHDF-Ad	bronchial
49	chr6:143160200-143161200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr6:143160200-143161200	Enhancers	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links