Variant report

Variant	rs9305659
Chromosome Location	chr21:40380071-40380072
allele	A/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	CEBPB	chr21:40379314-40380097	MCF-7	breast:	n/a	n/a
2	ZNF143	chr21:40380061-40380159	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:40379466..40381307-chr21:40382191..40384839,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PSMG1-6	chr21:40380028-40380157	ENSG00000237721

Variant related genes	Relation type
ENSG00000235888	TF binding region
ENSG00000237721	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2836821	0.91[ASN][1000 genomes]
rs2836823	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs59760205	0.82[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	nsv1062425	chr21:40172471-40380976	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544442	chr21:40172471-40380976	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv587477	chr21:40228920-40512004	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv1061831	chr21:40376316-40583555	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv544443	chr21:40376316-40583555	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40366400-40381600	Weak transcription	Psoas Muscle	Psoas
2	chr21:40372000-40385000	Weak transcription	Pancreas	Pancrea
3	chr21:40374000-40380400	Enhancers	Adipose Nuclei	Adipose
4	chr21:40374600-40380400	Enhancers	Fetal Muscle Leg	muscle
5	chr21:40374800-40381000	Enhancers	Fetal Thymus	thymus
6	chr21:40375800-40380400	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr21:40376000-40381200	Enhancers	Fetal Muscle Trunk	muscle
8	chr21:40376000-40381200	Enhancers	Placenta	Placenta
9	chr21:40376000-40384600	Enhancers	Lung	lung
10	chr21:40376600-40380200	Weak transcription	Fetal Kidney	kidney
11	chr21:40376600-40380400	Enhancers	Rectal Mucosa Donor 29	rectum
12	chr21:40376600-40383200	Enhancers	Fetal Lung	lung
13	chr21:40376800-40380400	Enhancers	Colonic Mucosa	Colon
14	chr21:40377400-40380600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr21:40377400-40381600	Weak transcription	Aorta	Aorta
16	chr21:40377600-40382400	Weak transcription	Fetal Intestine Large	intestine
17	chr21:40377600-40384200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr21:40377600-40384600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr21:40377800-40383000	Weak transcription	Thymus	Thymus
20	chr21:40378400-40381800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr21:40378400-40382600	Weak transcription	Right Ventricle	heart
22	chr21:40378400-40383200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr21:40378400-40385000	Weak transcription	Esophagus	oesophagus
24	chr21:40378600-40380200	Enhancers	NHEK	skin
25	chr21:40378600-40394600	Weak transcription	Gastric	stomach
26	chr21:40378800-40383000	Weak transcription	Dnd41	blood
27	chr21:40379000-40380600	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr21:40379200-40380600	Weak transcription	Brain Hippocampus Middle	brain
29	chr21:40379200-40381200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr21:40379200-40381600	Weak transcription	Left Ventricle	heart
31	chr21:40379200-40382400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr21:40379200-40382600	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr21:40379200-40385000	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr21:40379200-40386000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr21:40379200-40392600	Weak transcription	Duodenum Mucosa	Duodenum
36	chr21:40379400-40380600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr21:40379400-40380600	Enhancers	Monocytes-CD14+_RO01746	blood
38	chr21:40379400-40381000	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr21:40379400-40382600	Weak transcription	Primary B cells from cord blood	blood
40	chr21:40379600-40380600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr21:40379600-40381600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr21:40379600-40382800	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr21:40379800-40380200	Weak transcription	Right Atrium	heart
44	chr21:40379800-40381600	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr21:40379800-40382600	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr21:40379800-40383200	Enhancers	HepG2	liver
47	chr21:40380000-40380200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr21:40380000-40380400	Enhancers	Primary hematopoietic stem cells	blood
49	chr21:40380000-40380400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr21:40380000-40380400	Enhancers	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links