Variant report

Variant	rs1228184
Chromosome Location	chr3:100060135-100060136
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:100051539..100055958-chr3:100056037..100061247,9	MCF-7	breast:
2	chr3:100058351..100061697-chr3:100061751..100064533,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114021	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10936180	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1123578	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1214380	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1214381	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1530283	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs166747	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277620	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277622	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs277623	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277626	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs277628	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277629	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs277630	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs277633	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277634	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs277635	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277638	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs277642	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277644	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs277651	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs372438	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3772692	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3806615	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs392066	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs402870	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs413425	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs431069	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs432715	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6780662	0.88[ASN][1000 genomes]
rs6791102	0.88[ASN][1000 genomes]
rs6794955	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7616634	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7641630	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[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	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1003924	chr3:99933762-100112690	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 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	chr3:100054000-100065000	Weak transcription	Spleen	Spleen
2	chr3:100054200-100081000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:100054400-100067600	Weak transcription	Psoas Muscle	Psoas
4	chr3:100054600-100060200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:100054600-100063000	Weak transcription	Brain Substantia Nigra	brain
6	chr3:100054600-100064200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:100054600-100064400	Weak transcription	Thymus	Thymus
8	chr3:100054600-100102600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr3:100054800-100060200	Weak transcription	Right Ventricle	heart
10	chr3:100054800-100060600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr3:100054800-100061400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr3:100054800-100062200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr3:100054800-100062800	Weak transcription	HUVEC	blood vessel
14	chr3:100054800-100064200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:100054800-100064600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr3:100054800-100064600	Weak transcription	NHLF	lung
17	chr3:100054800-100067200	Weak transcription	Esophagus	oesophagus
18	chr3:100054800-100067400	Weak transcription	Small Intestine	intestine
19	chr3:100054800-100067600	Weak transcription	Colonic Mucosa	Colon
20	chr3:100054800-100068600	Weak transcription	Pancreas	Pancrea
21	chr3:100054800-100069000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr3:100054800-100081000	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr3:100054800-100097200	Weak transcription	Stomach Mucosa	stomach
24	chr3:100054800-100102200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr3:100055000-100060200	Weak transcription	Fetal Kidney	kidney
26	chr3:100055000-100060600	Weak transcription	GM12878-XiMat	blood
27	chr3:100055000-100062800	Weak transcription	Hela-S3	cervix
28	chr3:100055000-100068200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr3:100055000-100068600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr3:100055000-100082400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr3:100055200-100062600	Weak transcription	K562	blood
32	chr3:100055200-100068200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr3:100055200-100071000	Weak transcription	HepG2	liver
34	chr3:100056600-100061200	Strong transcription	Fetal Stomach	stomach
35	chr3:100056800-100061200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr3:100057000-100060400	Strong transcription	Primary hematopoietic stem cells	blood
37	chr3:100057000-100060600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:100057000-100061200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:100057000-100061200	Strong transcription	Fetal Muscle Trunk	muscle
40	chr3:100057000-100061200	Strong transcription	Fetal Muscle Leg	muscle
41	chr3:100057000-100069200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:100057000-100069600	Strong transcription	Dnd41	blood
43	chr3:100057200-100060600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr3:100057200-100060800	Strong transcription	NHEK	skin
45	chr3:100057200-100061000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:100057200-100061000	Strong transcription	Primary B cells from cord blood	blood
47	chr3:100057200-100061200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr3:100057200-100061200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr3:100057200-100061800	Strong transcription	Osteobl	bone
50	chr3:100057200-100066800	Strong transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links