Variant report

Variant	rs2544884
Chromosome Location	chr5:154331817-154331818
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	chr5:154329203..154332066-chr5:154336166..154338963,2	K562	blood:
2	chr5:154328491..154332066-chr5:154334049..154337666,3	K562	blood:

Variant related genes	Relation type
ENSG00000082515	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1035368	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10515727	0.83[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes]
rs12187890	0.80[AMR][1000 genomes]
rs12187921	0.82[CHB][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap]
rs12188498	1.00[TSI][hapmap]
rs12188828	1.00[CEU][hapmap];0.82[CHB][hapmap];0.80[EUR][1000 genomes]
rs12300	0.87[CEU][hapmap];0.95[GIH][hapmap];0.83[LWK][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1421815	1.00[TSI][hapmap]
rs1421819	1.00[TSI][hapmap];0.80[AMR][1000 genomes]
rs164195	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17096232	1.00[TSI][hapmap]
rs17116411	0.80[EUR][1000 genomes]
rs17116414	0.80[EUR][1000 genomes]
rs17116417	1.00[TSI][hapmap]
rs17116421	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17116433	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs17116442	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17116534	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs180846	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs186971	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1974776	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1974777	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2042168	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2112223	1.00[CEU][hapmap];0.84[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2161128	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2258437	0.93[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.80[LWK][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2431184	0.85[ASN][1000 genomes]
rs2544859	0.93[CEU][hapmap];0.82[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2544866	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2544874	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2544875	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2544876	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2544880	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2560063	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2644743	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2644744	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2644746	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688186	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2688187	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2688188	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2688189	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2688190	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2688191	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2688193	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2688194	0.81[EUR][1000 genomes]
rs2688195	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2688198	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2688199	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2688200	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2688201	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2688206	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2688208	1.00[CEU][hapmap];0.83[YRI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs348739	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs348748	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs348749	0.86[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs348750	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs348751	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs348752	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs348754	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3776984	1.00[TSI][hapmap]
rs39614	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4354100	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs454161	0.85[ASN][1000 genomes]
rs4958771	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55770418	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56374414	0.83[EUR][1000 genomes]
rs58415346	0.80[EUR][1000 genomes]
rs59525998	0.83[EUR][1000 genomes]
rs59749917	0.83[EUR][1000 genomes]
rs6865950	1.00[TSI][hapmap]
rs6879277	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6884416	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6895741	1.00[TSI][hapmap]
rs702742	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73276742	0.80[EUR][1000 genomes]
rs73280705	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73807206	0.80[AMR][1000 genomes]
rs73807213	0.80[AMR][1000 genomes]
rs7716019	1.00[TSI][hapmap]
rs7723269	0.80[EUR][1000 genomes]
rs816717	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs816718	1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs816720	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs816722	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs816743	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs816747	0.85[CHD][hapmap]
rs888694	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs960499	0.85[CHD][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2544884	EBF1	cis	parietal	SCAN
rs2544884	ANXA6	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154321200-154337400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:154321200-154338000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr5:154321400-154336400	Weak transcription	Placenta	Placenta
4	chr5:154321400-154338000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr5:154321400-154338200	Weak transcription	Lung	lung
6	chr5:154321400-154338600	Weak transcription	Gastric	stomach
7	chr5:154321400-154338800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr5:154321400-154339000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:154321400-154346000	Weak transcription	Colonic Mucosa	Colon
10	chr5:154321600-154336000	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr5:154321600-154336600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr5:154321600-154337400	Weak transcription	Fetal Intestine Small	intestine
13	chr5:154321600-154337400	Weak transcription	Ovary	ovary
14	chr5:154321600-154338000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr5:154321600-154338200	Weak transcription	Aorta	Aorta
16	chr5:154321600-154338800	Weak transcription	Fetal Kidney	kidney
17	chr5:154321600-154340000	Weak transcription	HSMMtube	muscle
18	chr5:154321600-154343400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr5:154321600-154345600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr5:154321800-154336200	Weak transcription	NH-A	brain
21	chr5:154321800-154336400	Weak transcription	Fetal Thymus	thymus
22	chr5:154321800-154338600	Weak transcription	Fetal Muscle Leg	muscle
23	chr5:154321800-154352200	Weak transcription	Right Ventricle	heart
24	chr5:154322000-154350000	Weak transcription	Fetal Brain Male	brain
25	chr5:154322200-154336600	Weak transcription	Osteobl	bone
26	chr5:154322200-154338800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr5:154322400-154335200	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr5:154322400-154335800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr5:154322400-154336200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr5:154322400-154336200	Weak transcription	Fetal Intestine Large	intestine
31	chr5:154322400-154336400	Weak transcription	HSMM	muscle
32	chr5:154322400-154336600	Weak transcription	Rectal Smooth Muscle	rectum
33	chr5:154322400-154337800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr5:154322400-154338400	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr5:154322400-154338600	Weak transcription	NHLF	lung
36	chr5:154322400-154338800	Weak transcription	HMEC	breast
37	chr5:154322400-154338800	Weak transcription	NHDF-Ad	bronchial
38	chr5:154322400-154339000	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr5:154322400-154349600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr5:154322600-154335800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr5:154322600-154336600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr5:154322600-154337800	Weak transcription	Fetal Lung	lung
43	chr5:154322600-154364600	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr5:154322800-154346000	Weak transcription	Colon Smooth Muscle	Colon
45	chr5:154323000-154335400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr5:154323000-154336800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr5:154323000-154337600	Weak transcription	Thymus	Thymus
48	chr5:154323000-154337800	Weak transcription	Stomach Smooth Muscle	stomach
49	chr5:154323000-154338200	Weak transcription	Pancreas	Pancrea
50	chr5:154324800-154338600	Weak transcription	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links