Variant report

Variant	rs3099983
Chromosome Location	chr2:39054703-39054704
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39036853..39041014-chr2:39051745..39054794,3	K562	blood:
2	chr2:39053503..39057037-chr2:39058758..39062643,3	K562	blood:
3	chr2:38976908..38981867-chr2:39050395..39056507,16	K562	blood:
4	chr2:38970642..38974334-chr2:39052366..39056279,4	K562	blood:
5	chr2:38974988..38979943-chr2:39053736..39058253,10	K562	blood:
6	chr2:39053934..39056407-chr2:39351577..39353846,2	K562	blood:
7	chr2:39053503..39055563-chr2:39060007..39062643,2	K562	blood:

Variant related genes	Relation type
ENSG00000152147	Chromatin interaction
ENSG00000223922	Chromatin interaction
ENSG00000115875	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs3099986	0.81[AFR][1000 genomes]
rs3112148	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised 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 target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39006400-39085600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr2:39019000-39057800	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr2:39022000-39066800	Weak transcription	Stomach Mucosa	stomach
4	chr2:39026600-39079800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr2:39030600-39088200	Weak transcription	Fetal Heart	heart
6	chr2:39032800-39072800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr2:39037200-39055800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr2:39038200-39056000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:39038800-39095600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:39038800-39102200	Weak transcription	Gastric	stomach
11	chr2:39039000-39085400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:39039000-39090000	Weak transcription	Esophagus	oesophagus
13	chr2:39039000-39101200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr2:39039000-39102000	Weak transcription	Colonic Mucosa	Colon
15	chr2:39040000-39069000	Strong transcription	Fetal Muscle Leg	muscle
16	chr2:39040600-39056000	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr2:39042800-39063000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr2:39042800-39080600	Weak transcription	Small Intestine	intestine
19	chr2:39043600-39079800	Weak transcription	Right Ventricle	heart
20	chr2:39044800-39056800	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr2:39046000-39073200	Weak transcription	Pancreas	Pancrea
22	chr2:39046200-39070200	Weak transcription	NHLF	lung
23	chr2:39046400-39057200	Weak transcription	HepG2	liver
24	chr2:39048000-39055600	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr2:39048400-39060800	Strong transcription	Fetal Stomach	stomach
26	chr2:39049000-39056000	Strong transcription	Fetal Intestine Small	intestine
27	chr2:39049400-39054800	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:39049400-39055400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr2:39049600-39055600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr2:39049600-39055600	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr2:39049600-39056200	Strong transcription	Fetal Intestine Large	intestine
32	chr2:39049800-39056000	Strong transcription	Brain Germinal Matrix	brain
33	chr2:39050000-39055600	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr2:39050000-39055600	Strong transcription	Dnd41	blood
35	chr2:39050200-39054800	Strong transcription	K562	blood
36	chr2:39050400-39062800	Weak transcription	Thymus	Thymus
37	chr2:39050400-39063800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr2:39050400-39072800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr2:39050400-39079800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr2:39050400-39079800	Weak transcription	Spleen	Spleen
41	chr2:39050400-39088000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr2:39051000-39068600	Weak transcription	HMEC	breast
43	chr2:39052000-39061800	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr2:39052200-39068600	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr2:39053000-39054800	Weak transcription	Hela-S3	cervix
46	chr2:39053000-39057200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr2:39053200-39068600	Weak transcription	Brain Substantia Nigra	brain
48	chr2:39053200-39069600	Weak transcription	HUVEC	blood vessel
49	chr2:39053600-39054800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr2:39053600-39055000	Weak transcription	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links