Variant report

Variant	rs197462
Chromosome Location	chr6:143081847-143081848
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:143077693..143080648-chr6:143080861..143082747,2	MCF-7	breast:
2	chr6:143080311..143082385-chr6:143264907..143266510,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000010818	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs197460	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs197464	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs197472	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs197482	1.00[JPT][hapmap];0.86[MEX][hapmap]
rs3383	0.83[CEU][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv830828	chr6:142970134-143116517	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	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:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:143072800-143094800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr6:143072800-143095200	Strong transcription	Fetal Thymus	thymus
3	chr6:143072800-143095400	Weak transcription	Fetal Kidney	kidney
4	chr6:143073000-143083800	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr6:143073000-143090800	Weak transcription	Right Atrium	heart
6	chr6:143073000-143096000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr6:143073600-143086400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr6:143074000-143086600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr6:143074000-143086800	Strong transcription	Adipose Nuclei	Adipose
10	chr6:143074000-143094000	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr6:143074200-143083000	Strong transcription	GM12878-XiMat	blood
12	chr6:143074800-143095800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:143075000-143082800	Weak transcription	Psoas Muscle	Psoas
14	chr6:143075000-143091000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:143075200-143083000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr6:143076200-143082200	Strong transcription	Primary B cells from cord blood	blood
17	chr6:143076200-143084200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr6:143076400-143082200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
19	chr6:143076600-143083000	Strong transcription	Primary T cells from cord blood	blood
20	chr6:143076800-143083800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr6:143077000-143082800	Strong transcription	Liver	Liver
22	chr6:143077000-143085000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr6:143077200-143082400	Strong transcription	Primary B cells from peripheral blood	blood
24	chr6:143077400-143082000	Strong transcription	Fetal Lung	lung
25	chr6:143077400-143082000	Strong transcription	Stomach Smooth Muscle	stomach
26	chr6:143077400-143083200	Strong transcription	Fetal Muscle Trunk	muscle
27	chr6:143077400-143084800	Strong transcription	Thymus	Thymus
28	chr6:143077800-143083200	Strong transcription	Left Ventricle	heart
29	chr6:143078000-143082400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr6:143078200-143082200	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr6:143078200-143083000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr6:143078200-143096200	Strong transcription	Primary hematopoietic stem cells	blood
33	chr6:143078400-143082400	Strong transcription	HMEC	breast
34	chr6:143078400-143083000	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr6:143078400-143083000	Weak transcription	Hela-S3	cervix
36	chr6:143078400-143083200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr6:143078400-143084200	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr6:143078600-143082800	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr6:143078600-143082800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr6:143078600-143084200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr6:143078600-143084800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr6:143078800-143082200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr6:143078800-143082200	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr6:143078800-143082400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr6:143078800-143082400	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr6:143078800-143083400	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr6:143079000-143082200	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr6:143079000-143082200	Strong transcription	Fetal Intestine Large	intestine
49	chr6:143079000-143082200	Strong transcription	Dnd41	blood
50	chr6:143079000-143082600	Strong transcription	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links