Variant report

Variant	rs1549767
Chromosome Location	chr2:128259371-128259372
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:128257904..128259935-chr2:128260195..128263144,2	K562	blood:
2	chr2:128259205..128261757-chr2:128272398..128274908,2	K562	blood:
3	chr2:128258277..128260022-chr2:128274058..128277038,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MAP3K2-4	chr2:128258673-128259739	NONHSAT074169

Variant related genes	Relation type
ENSG00000163166	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10190872	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10206221	0.87[ASN][1000 genomes]
rs12470481	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12475217	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12621149	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12987418	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13397441	0.85[ASN][1000 genomes]
rs13399231	0.92[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs13415053	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs17015347	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs17015399	0.84[ASN][1000 genomes]
rs173013	0.93[ASN][1000 genomes]
rs17522960	0.87[ASN][1000 genomes]
rs1864552	0.80[CEU][hapmap]
rs2078028	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2163348	0.80[CEU][hapmap]
rs2176595	0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2249646	0.87[ASN][1000 genomes]
rs2460106	0.82[CEU][hapmap]
rs2566564	0.83[ASN][1000 genomes]
rs2679402	0.97[ASN][1000 genomes]
rs2679407	0.87[ASN][1000 genomes]
rs2679409	0.82[CEU][hapmap]
rs334137	0.80[CEU][hapmap]
rs334138	0.82[CEU][hapmap]
rs334139	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs334140	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs334142	0.87[ASN][1000 genomes]
rs334143	0.81[CEU][hapmap]
rs334144	0.82[CEU][hapmap]
rs334146	0.82[CEU][hapmap]
rs334147	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs334148	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs334149	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs334150	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs334151	0.80[CEU][hapmap]
rs334152	0.82[CEU][hapmap]
rs334153	0.97[ASN][1000 genomes]
rs334155	0.97[ASN][1000 genomes]
rs334156	0.82[CEU][hapmap]
rs334158	0.80[CEU][hapmap]
rs334159	0.81[CEU][hapmap]
rs334160	0.80[CEU][hapmap]
rs334162	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3732208	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4423553	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs4662582	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55981410	0.82[ASN][1000 genomes]
rs56217122	0.87[ASN][1000 genomes]
rs56234754	0.83[ASN][1000 genomes]
rs58462277	0.96[ASN][1000 genomes]
rs59934067	0.97[ASN][1000 genomes]
rs61342606	0.83[ASN][1000 genomes]
rs6707186	0.82[ASN][1000 genomes]
rs6707425	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6713317	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs6722447	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6727506	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs6731270	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6734816	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6748790	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6757654	0.83[ASN][1000 genomes]
rs72958594	0.97[ASN][1000 genomes]
rs72958600	0.97[ASN][1000 genomes]
rs7570609	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs7572181	0.85[ASN][1000 genomes]
rs7574209	0.87[ASN][1000 genomes]
rs7574215	0.87[ASN][1000 genomes]
rs7576217	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7582598	0.80[CEU][hapmap]
rs7598346	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7603777	0.97[ASN][1000 genomes]
rs777547	0.97[ASN][1000 genomes]
rs777549	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs777550	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs777551	0.97[ASN][1000 genomes]
rs777554	0.80[CEU][hapmap]
rs777557	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs777558	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs777559	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs777561	0.93[ASN][1000 genomes]
rs777562	0.92[ASN][1000 genomes]
rs777563	0.92[ASN][1000 genomes]
rs777569	0.82[CEU][hapmap]
rs9287540	0.90[CEU][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	nsv875014	chr2:128178415-128328375	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128223600-128268800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:128235200-128270000	Strong transcription	Dnd41	blood
3	chr2:128237400-128262400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:128237600-128263200	Strong transcription	Adipose Nuclei	Adipose
5	chr2:128237600-128263200	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr2:128237600-128263400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr2:128237600-128263400	Strong transcription	Fetal Thymus	thymus
8	chr2:128237800-128263200	Strong transcription	Liver	Liver
9	chr2:128237800-128263200	Strong transcription	HUVEC	blood vessel
10	chr2:128237800-128263400	Strong transcription	Placenta	Placenta
11	chr2:128238400-128262400	Strong transcription	NH-A	brain
12	chr2:128238800-128260400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr2:128239200-128263400	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr2:128239200-128264800	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr2:128239400-128264400	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr2:128239400-128266200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:128239400-128266400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr2:128239800-128261800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:128240000-128263400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr2:128240200-128263600	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr2:128240400-128263800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:128240600-128265600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr2:128241000-128263200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:128242000-128262600	Strong transcription	Fetal Brain Female	brain
25	chr2:128242600-128263200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr2:128242600-128263200	Strong transcription	HMEC	breast
27	chr2:128242800-128262200	Strong transcription	HSMM	muscle
28	chr2:128244000-128263200	Strong transcription	Primary B cells from cord blood	blood
29	chr2:128244600-128262200	Strong transcription	Osteobl	bone
30	chr2:128244600-128263600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr2:128244600-128263800	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr2:128244600-128263800	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr2:128244600-128263800	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr2:128244600-128263800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr2:128245000-128262200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:128245200-128263600	Strong transcription	Primary B cells from peripheral blood	blood
37	chr2:128245800-128263200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr2:128245800-128263400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr2:128246200-128263400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr2:128246200-128271800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr2:128248000-128264800	Weak transcription	Fetal Heart	heart
42	chr2:128248800-128263800	Strong transcription	Fetal Intestine Large	intestine
43	chr2:128249000-128263200	Strong transcription	Duodenum Mucosa	Duodenum
44	chr2:128250600-128259800	Weak transcription	Small Intestine	intestine
45	chr2:128251000-128259800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr2:128251000-128262200	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr2:128252200-128259600	Weak transcription	Colon Smooth Muscle	Colon
48	chr2:128252200-128262200	Weak transcription	Spleen	Spleen
49	chr2:128252200-128262400	Weak transcription	Pancreas	Pancrea
50	chr2:128252400-128259400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links