Variant report

Variant	rs2255317
Chromosome Location	chr8:99044528-99044529
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	chr8:99044015..99047319-chr8:99128831..99131004,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C8orf47-2	chr8:99043670-99044545	NONHSAT127893

Variant related genes	Relation type
ENSG00000104356	Chromatin interaction
ENSG00000132541	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10088117	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs10093417	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12334735	0.88[AFR][1000 genomes]
rs13439751	0.94[YRI][hapmap];0.86[AFR][1000 genomes]
rs1378122	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1454713	0.88[JPT][hapmap]
rs2010016	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2061052	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2331692	1.00[ASW][hapmap];0.80[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.94[TSI][hapmap];0.94[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2444857	0.82[JPT][hapmap]
rs2444859	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2444866	0.89[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes]
rs2444885	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2444894	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2444898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2447488	0.81[ASN][1000 genomes]
rs2513806	0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2513808	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2513815	0.91[ASN][1000 genomes]
rs2513817	0.89[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap];0.81[ASN][1000 genomes]
rs2513819	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2513823	0.81[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28638239	0.80[AFR][1000 genomes]
rs2959642	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73701228	0.88[AFR][1000 genomes]
rs748324	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][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	nsv1032904	chr8:98756076-99476925	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv539687	chr8:98756076-99476925	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:99008400-99045000	Weak transcription	Colonic Mucosa	Colon
2	chr8:99021200-99053600	Weak transcription	A549	lung
3	chr8:99022400-99055200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr8:99024000-99054800	Weak transcription	Right Ventricle	heart
5	chr8:99024200-99055000	Weak transcription	Fetal Brain Male	brain
6	chr8:99024200-99056000	Weak transcription	Spleen	Spleen
7	chr8:99025000-99052800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr8:99025200-99045400	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr8:99025400-99045200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr8:99027600-99045400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr8:99028800-99045400	Weak transcription	Fetal Brain Female	brain
12	chr8:99029000-99053600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr8:99030000-99045000	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr8:99030000-99045200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr8:99030600-99053400	Weak transcription	Pancreas	Pancrea
16	chr8:99030600-99056800	Weak transcription	Aorta	Aorta
17	chr8:99030800-99046400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr8:99031000-99055400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr8:99032200-99045800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr8:99032400-99046800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr8:99033600-99045400	Weak transcription	HSMM	muscle
22	chr8:99033800-99045600	Weak transcription	Thymus	Thymus
23	chr8:99033800-99045600	Weak transcription	HMEC	breast
24	chr8:99033800-99054800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr8:99033800-99055200	Weak transcription	Small Intestine	intestine
26	chr8:99033800-99055600	Weak transcription	Left Ventricle	heart
27	chr8:99034000-99045800	Weak transcription	GM12878-XiMat	blood
28	chr8:99034200-99050800	Weak transcription	Colon Smooth Muscle	Colon
29	chr8:99034200-99054200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr8:99034200-99054800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr8:99035400-99047200	Strong transcription	Fetal Muscle Trunk	muscle
32	chr8:99035600-99045200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr8:99035600-99046000	Strong transcription	Fetal Muscle Leg	muscle
34	chr8:99036000-99047400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr8:99036200-99045000	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr8:99036400-99048600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr8:99036800-99053200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr8:99037200-99049200	Weak transcription	Brain Anterior Caudate	brain
39	chr8:99037200-99053200	Weak transcription	Fetal Intestine Small	intestine
40	chr8:99037600-99045400	Weak transcription	Primary B cells from cord blood	blood
41	chr8:99037600-99045400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr8:99037600-99052400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr8:99037600-99054800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr8:99037600-99056400	Weak transcription	Lung	lung
45	chr8:99038000-99047200	Strong transcription	Placenta Amnion	Placenta Amnion
46	chr8:99039000-99048800	Strong transcription	Duodenum Mucosa	Duodenum
47	chr8:99039200-99053000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr8:99040200-99048600	Weak transcription	NHLF	lung
49	chr8:99040400-99046800	Strong transcription	Primary B cells from peripheral blood	blood
50	chr8:99040400-99047000	Strong transcription	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links