Variant report

Variant	rs4973063
Chromosome Location	chr2:233926201-233926202
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:233925658..233927822-chr2:233939006..233941097,2	K562	blood:

Variant related genes	Relation type
ENSG00000168918	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1141328	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12994169	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28773607	0.80[EUR][1000 genomes]
rs28854328	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34218488	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35140857	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3935584	0.96[CEU][hapmap];0.85[TSI][hapmap]
rs4073363	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs4257390	0.88[CEU][hapmap];0.81[TSI][hapmap]
rs7558755	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7585583	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv876009	chr2:233799400-233996429	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv876012	chr2:233899377-233996429	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv520361	chr2:233926201-233929545	Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4973063	B3GNT7	cis	parietal	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233914400-233926600	Weak transcription	HSMMtube	muscle
2	chr2:233923000-233927800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr2:233924400-233926800	Enhancers	K562	blood
4	chr2:233924400-233927200	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr2:233924400-233927200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
6	chr2:233924400-233928800	Active TSS	Brain Hippocampus Middle	brain
7	chr2:233924600-233927000	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr2:233924600-233927000	Active TSS	Stomach Smooth Muscle	stomach
9	chr2:233924600-233928000	Active TSS	Brain Anterior Caudate	brain
10	chr2:233924600-233929200	Active TSS	Rectal Smooth Muscle	rectum
11	chr2:233924800-233926400	Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr2:233924800-233926400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
13	chr2:233924800-233926800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
14	chr2:233924800-233927000	Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr2:233924800-233927000	Active TSS	Rectal Mucosa Donor 31	rectum
16	chr2:233924800-233927200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr2:233924800-233927200	Active TSS	Brain Cingulate Gyrus	brain
18	chr2:233924800-233927200	Active TSS	Small Intestine	intestine
19	chr2:233924800-233927400	Active TSS	Liver	Liver
20	chr2:233924800-233927400	Flanking Active TSS	Fetal Muscle Trunk	muscle
21	chr2:233924800-233927400	Flanking Active TSS	Fetal Muscle Leg	muscle
22	chr2:233924800-233927400	Flanking Active TSS	HUVEC	blood vessel
23	chr2:233924800-233927600	Active TSS	Sigmoid Colon	Sigmoid Colon
24	chr2:233924800-233929800	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr2:233925000-233926400	Active TSS	Primary monocytes fromperipheralblood	blood
26	chr2:233925000-233926400	Active TSS	Primary B cells from peripheral blood	blood
27	chr2:233925000-233926400	Flanking Active TSS	Fetal Stomach	stomach
28	chr2:233925000-233926400	Active TSS	Gastric	stomach
29	chr2:233925000-233926600	Active TSS	GM12878-XiMat	blood
30	chr2:233925000-233926800	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr2:233925000-233926800	Flanking Active TSS	Fetal Intestine Small	intestine
32	chr2:233925000-233927000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
33	chr2:233925000-233927400	Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr2:233925000-233927400	Active TSS	Esophagus	oesophagus
35	chr2:233925200-233926600	Active TSS	Brain Substantia Nigra	brain
36	chr2:233925200-233927000	Active TSS	Colon Smooth Muscle	Colon
37	chr2:233925200-233927200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:233925200-233927800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr2:233925200-233930000	Enhancers	Stomach Mucosa	stomach
40	chr2:233925400-233926400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
41	chr2:233925400-233926600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr2:233925400-233926600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
43	chr2:233925400-233926600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr2:233925400-233927200	Flanking Active TSS	Dnd41	blood
45	chr2:233925400-233928400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr2:233925400-233930000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
47	chr2:233925600-233926600	Weak transcription	Pancreas	Pancrea
48	chr2:233925600-233926800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr2:233925600-233927000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
50	chr2:233925600-233927400	Flanking Active TSS	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links