Variant report

Variant	rs10008275
Chromosome Location	chr4:147254969-147254970
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:147254547..147257377-chr4:147259136..147260909,2	K562	blood:
2	chr4:147162002..147168172-chr4:147253902..147262824,27	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TTC29-2	chr4:147254244-147255067	ucscGeneNc_uc010ioy_1

Variant related genes	Relation type
ENSG00000251010	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10010528	0.90[CHB][hapmap];0.88[JPT][hapmap];0.98[ASN][1000 genomes]
rs10013722	0.98[ASN][1000 genomes]
rs10027135	0.94[ASN][1000 genomes]
rs10032088	0.81[CHB][hapmap]
rs11735261	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs11736003	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11737121	0.91[CHB][hapmap];0.92[ASN][1000 genomes]
rs11939345	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11947781	0.93[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17021396	0.94[CEU][hapmap];0.91[CHB][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2200474	0.91[CHB][hapmap];0.92[ASN][1000 genomes]
rs28521842	0.98[ASN][1000 genomes]
rs28625764	0.94[ASN][1000 genomes]
rs4835033	0.93[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4835292	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4835294	0.90[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs4835296	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4835297	0.93[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4835299	0.94[CEU][hapmap];0.90[CHB][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55798872	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57713263	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6846294	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6846584	0.93[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6846846	0.92[ASN][1000 genomes]
rs6857911	0.93[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9784436	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9784437	0.87[CEU][hapmap];0.90[CHB][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9999381	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461675	chr4:147116864-147768206	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv595651	chr4:147116864-147768206	Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	esv3451660	chr4:147225135-147271246	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv3443192	chr4:147225234-147271217	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv3468025	chr4:147225279-147271172	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	esv3468026	chr4:147225279-147271172	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1033640	chr4:147232217-147531881	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:147212800-147264200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr4:147229600-147257400	Weak transcription	Ovary	ovary
3	chr4:147233000-147255000	Weak transcription	Aorta	Aorta
4	chr4:147241800-147255200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr4:147241800-147284800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr4:147242800-147255000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr4:147243000-147255000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:147244200-147255200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr4:147246200-147255000	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr4:147247600-147255000	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr4:147248800-147257200	Weak transcription	Fetal Intestine Large	intestine
12	chr4:147249800-147255400	Weak transcription	Small Intestine	intestine
13	chr4:147249800-147256000	Weak transcription	Lung	lung
14	chr4:147249800-147256400	Weak transcription	Left Ventricle	heart
15	chr4:147249800-147256600	Weak transcription	Esophagus	oesophagus
16	chr4:147250600-147255000	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr4:147252400-147256000	Weak transcription	Hela-S3	cervix
18	chr4:147252600-147256000	Weak transcription	Fetal Lung	lung
19	chr4:147252600-147256400	Weak transcription	HUVEC	blood vessel
20	chr4:147252800-147256400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr4:147254400-147255400	Enhancers	Duodenum Mucosa	Duodenum
22	chr4:147254400-147256000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:147254400-147256000	Enhancers	A549	lung
24	chr4:147254400-147256800	Flanking Active TSS	GM12878-XiMat	blood
25	chr4:147254600-147255000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr4:147254600-147255000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr4:147254600-147255000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:147254600-147255000	Enhancers	Gastric	stomach
29	chr4:147254600-147255000	Flanking Active TSS	NHEK	skin
30	chr4:147254600-147255200	Flanking Active TSS	NH-A	brain
31	chr4:147254600-147255200	Active TSS	NHLF	lung
32	chr4:147254600-147255400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr4:147254600-147255400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr4:147254600-147255400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
35	chr4:147254600-147255400	Flanking Active TSS	Osteobl	bone
36	chr4:147254600-147255600	Enhancers	HMEC	breast
37	chr4:147254600-147258000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr4:147254800-147255000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr4:147254800-147255200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr4:147254800-147255200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr4:147254800-147255200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr4:147254800-147255200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
43	chr4:147254800-147255200	Enhancers	Thymus	Thymus
44	chr4:147254800-147255200	Flanking Active TSS	HSMM	muscle
45	chr4:147254800-147255200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr4:147254800-147255400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr4:147254800-147255400	Enhancers	Fetal Thymus	thymus
48	chr4:147254800-147255400	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr4:147254800-147255400	Enhancers	Stomach Mucosa	stomach
50	chr4:147254800-147255400	Flanking Active TSS	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links