Variant report

Variant	rs2544880
Chromosome Location	chr5:154265119-154265120
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	chr5:154236554..154241107-chr5:154261832..154268242,6	MCF-7	breast:
2	chr5:154256944..154260356-chr5:154260971..154266243,8	K562	blood:

Variant related genes	Relation type
ENSG00000170271	Chromatin interaction
ENSG00000155508	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1035368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10515727	0.84[MEX][hapmap];1.00[TSI][hapmap]
rs11167705	0.84[ASN][1000 genomes]
rs12187921	1.00[CHB][hapmap];1.00[TSI][hapmap]
rs12188498	1.00[TSI][hapmap]
rs12188828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12300	0.93[ASW][hapmap];0.87[CEU][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[LWK][hapmap];0.94[MKK][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1421813	0.80[AMR][1000 genomes]
rs1421815	1.00[TSI][hapmap]
rs1421819	1.00[TSI][hapmap]
rs164195	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17096232	1.00[TSI][hapmap]
rs17116409	1.00[TSI][hapmap]
rs17116411	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17116414	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17116417	1.00[TSI][hapmap]
rs17116421	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17116433	1.00[CHB][hapmap]
rs17116442	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17116534	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];0.89[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs180846	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs186971	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1974776	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1974777	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2042168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2112223	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2161128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2258437	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2396999	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs2431184	0.92[ASN][1000 genomes]
rs2544859	0.93[CEU][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2544860	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2544866	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2544874	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2544875	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2544876	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2544884	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]
rs255529	0.86[ASN][1000 genomes]
rs2560063	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2644743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2644744	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2644746	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2688186	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688187	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2688188	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688189	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2688190	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2688191	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688193	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688194	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2688195	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2688198	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];0.89[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2688199	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2688200	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2688201	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2688206	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2688208	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs32427	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs348739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs348748	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs348749	0.86[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs348750	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs348751	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs348752	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs348754	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3776984	1.00[TSI][hapmap]
rs39614	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4354100	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs454161	0.92[ASN][1000 genomes]
rs4958771	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55770418	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56374414	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58415346	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59525998	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59749917	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6580122	0.82[ASN][1000 genomes]
rs6865950	1.00[TSI][hapmap];0.80[AMR][1000 genomes]
rs6873483	0.81[ASN][1000 genomes]
rs6879277	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6884416	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6895741	1.00[TSI][hapmap]
rs702742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73276742	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73280705	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7709899	0.80[AMR][1000 genomes]
rs7716019	1.00[TSI][hapmap]
rs7723269	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7728194	0.82[EUR][1000 genomes]
rs816717	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs816718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs816720	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs816722	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs816734	0.88[ASN][1000 genomes]
rs816743	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs816747	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs888694	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs960499	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9942412	0.81[EUR][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2544880	EBF1	cis	parietal	SCAN
rs2544880	ANXA6	cis	parietal	SCAN
rs2544880	CNOT8	cis	brain	seeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154248600-154267600	Weak transcription	Right Atrium	heart
2	chr5:154255600-154266000	Weak transcription	NHLF	lung
3	chr5:154255800-154265200	Weak transcription	Fetal Kidney	kidney
4	chr5:154256000-154265200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr5:154256000-154266000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr5:154257000-154266000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr5:154257200-154265200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr5:154257600-154266000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr5:154258800-154265600	Weak transcription	Gastric	stomach
10	chr5:154258800-154265800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr5:154259000-154265200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr5:154259000-154265200	Weak transcription	HSMMtube	muscle
13	chr5:154259000-154265400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr5:154259000-154265400	Weak transcription	Fetal Thymus	thymus
15	chr5:154259000-154265400	Weak transcription	Right Ventricle	heart
16	chr5:154259000-154265800	Weak transcription	Pancreas	Pancrea
17	chr5:154259200-154266000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:154259400-154265800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr5:154259400-154265800	Weak transcription	Colonic Mucosa	Colon
20	chr5:154262000-154268400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr5:154262000-154268800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
22	chr5:154262200-154265600	Weak transcription	Esophagus	oesophagus
23	chr5:154262800-154268000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr5:154262800-154300800	Strong transcription	Fetal Brain Female	brain
25	chr5:154263000-154265800	Weak transcription	Left Ventricle	heart
26	chr5:154263800-154265200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
27	chr5:154263800-154266600	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
28	chr5:154263800-154267600	ZNF genes & repeats	Primary B cells from cord blood	blood
29	chr5:154263800-154268200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr5:154264000-154265200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr5:154264000-154266000	Strong transcription	Ovary	ovary
32	chr5:154264000-154266400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr5:154264000-154266400	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
34	chr5:154264000-154266400	ZNF genes & repeats	Fetal Intestine Small	intestine
35	chr5:154264000-154266600	ZNF genes & repeats	Thymus	Thymus
36	chr5:154264000-154266800	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
37	chr5:154264000-154266800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
38	chr5:154264000-154266800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
39	chr5:154264000-154266800	ZNF genes & repeats	Fetal Lung	lung
40	chr5:154264000-154267600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
41	chr5:154264000-154267600	ZNF genes & repeats	Fetal Muscle Leg	muscle
42	chr5:154264000-154268200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
43	chr5:154264000-154268200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
44	chr5:154264000-154268400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr5:154264000-154268600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
46	chr5:154264000-154272200	Strong transcription	HSMM	muscle
47	chr5:154264000-154276600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr5:154264000-154312800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr5:154264200-154265800	Weak transcription	Placenta	Placenta
50	chr5:154264200-154266200	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--

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