Variant report

Variant	rs8304
Chromosome Location	chr2:169630835-169630836
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:169628746..169631542-chr2:169795260..169797198,2	K562	blood:
2	chr2:169630763..169636990-chr2:169638094..169645299,10	K562	blood:
3	chr2:169629191..169630841-chr2:169776722..169777731,4	MCF-7	breast:
4	chr2:169629920..169631115-chr2:169776779..169777787,11	K562	blood:
5	chr2:169630102..169630887-chr2:169804877..169805660,3	MCF-7	breast:
6	chr2:169629254..169632077-chr2:169708619..169710261,2	K562	blood:
7	chr2:169629519..169633434-chr2:169651628..169656188,4	K562	blood:
8	chr2:169614606..169616373-chr2:169628281..169631112,2	K562	blood:
9	chr2:169629906..169631239-chr2:169776809..169777837,8	MCF-7	breast:
10	chr2:169630347..169631099-chr20:6143956..6144677,2	MCF-7	breast:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPC25-1	chr2:169628463-169631148	ENSG00000227617.2
2	lnc-SPC25-1	chr2:169628461-169631148	NONHSAT075331
3	lnc-SPC25-1	chr2:169628461-169631148	NONHSAT075332
4	lnc-SPC25-1	chr2:169628464-169631148	NONHSAT075333

No data

Variant related genes	Relation type
ENSG00000227617	Chromatin interaction
ENSG00000163072	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12692886	0.84[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13017628	1.00[CHB][hapmap]
rs1402840	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16855872	1.00[CHB][hapmap];0.83[CHD][hapmap];0.83[ASN][1000 genomes]
rs3845726	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs3845727	1.00[CHB][hapmap];0.85[CHD][hapmap];0.83[ASN][1000 genomes]
rs3856426	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3914920	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs4233821	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4668103	1.00[CHB][hapmap];0.84[GIH][hapmap];0.83[TSI][hapmap]
rs6433092	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7558965	1.00[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915920	chr2:168851960-169696591	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs8304	C2orf77	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:169597200-169635800	Weak transcription	Ovary	ovary
2	chr2:169606600-169632800	Weak transcription	Pancreas	Pancrea
3	chr2:169608200-169633800	Weak transcription	Psoas Muscle	Psoas
4	chr2:169608400-169632200	Weak transcription	HSMMtube	muscle
5	chr2:169608400-169633600	Weak transcription	Dnd41	blood
6	chr2:169609200-169636400	Weak transcription	Lung	lung
7	chr2:169609400-169633000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr2:169609600-169634200	Weak transcription	Fetal Brain Male	brain
9	chr2:169610800-169637400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:169611200-169636600	Weak transcription	HepG2	liver
11	chr2:169614400-169631800	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr2:169621600-169631000	Strong transcription	Fetal Thymus	thymus
13	chr2:169622200-169641400	Weak transcription	Small Intestine	intestine
14	chr2:169622400-169631400	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr2:169623400-169632600	Weak transcription	Right Ventricle	heart
16	chr2:169623400-169632800	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr2:169624400-169632800	Weak transcription	NHEK	skin
18	chr2:169624800-169632200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr2:169625400-169633000	Strong transcription	Primary T cells from cord blood	blood
20	chr2:169625600-169632400	Weak transcription	Fetal Intestine Small	intestine
21	chr2:169625600-169635400	Weak transcription	Fetal Stomach	stomach
22	chr2:169626400-169632200	Weak transcription	GM12878-XiMat	blood
23	chr2:169626600-169632000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr2:169626600-169632200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr2:169626600-169632200	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr2:169626600-169632400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr2:169626600-169632400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr2:169626600-169632400	Weak transcription	Duodenum Mucosa	Duodenum
29	chr2:169626600-169632600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:169626800-169631200	Enhancers	Fetal Heart	heart
31	chr2:169626800-169632000	Weak transcription	Fetal Muscle Leg	muscle
32	chr2:169626800-169633000	Weak transcription	Primary B cells from cord blood	blood
33	chr2:169626800-169633800	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr2:169626800-169641800	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr2:169627000-169632400	Weak transcription	Stomach Smooth Muscle	stomach
36	chr2:169627200-169632000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr2:169627400-169632400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr2:169627600-169631400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr2:169627600-169632400	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr2:169627800-169632400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr2:169627800-169636600	Weak transcription	Fetal Kidney	kidney
42	chr2:169628000-169631400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr2:169628000-169637000	Weak transcription	Hela-S3	cervix
44	chr2:169629200-169632200	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr2:169629400-169633600	Weak transcription	Fetal Intestine Large	intestine
46	chr2:169630000-169631000	Strong transcription	Brain Germinal Matrix	brain
47	chr2:169630000-169631000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr2:169630000-169631200	Flanking Active TSS	K562	blood
49	chr2:169630000-169632800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr2:169630200-169631000	Strong transcription	Fetal Brain Female	brain

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