Variant report

Variant	rs11966402
Chromosome Location	chr6:35422542-35422543
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:35418643..35423313-chr6:35462563..35468017,10	K562	blood:
2	chr6:35415085..35416689-chr6:35421187..35424185,2	K562	blood:
3	chr6:35415818..35424678-chr6:35432486..35440672,36	K562	blood:
4	chr6:35418617..35424875-chr6:35434196..35438070,12	MCF-7	breast:
5	chr6:35421073..35422894-chr6:35443794..35445610,2	K562	blood:
6	chr6:35258451..35260687-chr6:35421514..35424141,3	MCF-7	breast:
7	chr6:35262981..35267829-chr6:35418945..35424124,7	K562	blood:

Variant related genes	Relation type
ENSG00000198755	Chromatin interaction
ENSG00000007866	Chromatin interaction
ENSG00000065029	Chromatin interaction
ENSG00000023892	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs16876572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41270066	0.85[AFR][1000 genomes]
rs45558531	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73415611	0.98[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs73415612	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9658182	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830641	chr6:35282534-35440603	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
2	nsv602909	chr6:35356640-35423489	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv528351	chr6:35377922-35465786	Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 gene(s)	inside rSNPs	diseases
4	nsv885799	chr6:35378778-35442397	Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
5	nsv462908	chr6:35378778-35457396	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
6	nsv602910	chr6:35378778-35457396	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
7	nsv519370	chr6:35378778-35537406	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	72 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	chr6:35420800-35422800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:35420800-35423400	Weak transcription	Gastric	stomach
3	chr6:35420800-35423400	Weak transcription	Lung	lung
4	chr6:35420800-35423400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:35420800-35423600	Weak transcription	Left Ventricle	heart
6	chr6:35421000-35422800	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr6:35421000-35422800	Flanking Active TSS	NHEK	skin
8	chr6:35421000-35423000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr6:35421000-35427200	Weak transcription	Thymus	Thymus
10	chr6:35421000-35435400	Weak transcription	Colon Smooth Muscle	Colon
11	chr6:35421200-35422800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:35421200-35422800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:35421200-35422800	Enhancers	Adipose Nuclei	Adipose
14	chr6:35421200-35422800	Enhancers	Fetal Brain Male	brain
15	chr6:35421200-35423000	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr6:35421200-35423000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:35421200-35423400	Weak transcription	Spleen	Spleen
18	chr6:35421200-35425200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr6:35421200-35425600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr6:35421200-35425600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr6:35421200-35426200	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr6:35421200-35435200	Weak transcription	Brain Angular Gyrus	brain
23	chr6:35421200-35435400	Weak transcription	Brain Anterior Caudate	brain
24	chr6:35421400-35422600	Enhancers	Brain Germinal Matrix	brain
25	chr6:35421400-35422600	Enhancers	Fetal Stomach	stomach
26	chr6:35421400-35422800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr6:35421400-35422800	Enhancers	Brain Hippocampus Middle	brain
28	chr6:35421400-35422800	Enhancers	Fetal Lung	lung
29	chr6:35421400-35423000	Enhancers	H1 Cell Line	embryonic stem cell
30	chr6:35421400-35423000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:35421400-35423000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr6:35421400-35423000	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr6:35421400-35423000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:35421400-35423000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr6:35421400-35423000	Enhancers	Fetal Heart	heart
36	chr6:35421400-35423000	Enhancers	Fetal Muscle Leg	muscle
37	chr6:35421400-35423000	Enhancers	NHDF-Ad	bronchial
38	chr6:35421400-35423400	Weak transcription	Primary B cells from peripheral blood	blood
39	chr6:35421400-35423400	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr6:35421400-35423400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr6:35421400-35423600	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr6:35421400-35424000	Weak transcription	Duodenum Mucosa	Duodenum
43	chr6:35421400-35424600	Weak transcription	Primary T cells from cord blood	blood
44	chr6:35421400-35424600	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr6:35421400-35424600	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr6:35421400-35425200	Weak transcription	Rectal Smooth Muscle	rectum
47	chr6:35421400-35425600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr6:35421400-35425800	Weak transcription	Brain Substantia Nigra	brain
49	chr6:35421400-35435400	Weak transcription	Colonic Mucosa	Colon
50	chr6:35421400-35435400	Weak transcription	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links