Variant report

Variant	rs348739
Chromosome Location	chr5:154300940-154300941
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:154298083..154301550-chr5:154315373..154317841,3	MCF-7	breast:
2	chr5:154299597..154302398-chr5:154315170..154317851,2	MCF-7	breast:
3	chr5:154297619..154302417-chr5:154303443..154308380,7	K562	blood:
4	chr5:154299302..154301553-chr5:154303443..154306130,2	K562	blood:

Variant related genes	Relation type
ENSG00000082516	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs1035368	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];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10515727	0.84[MEX][hapmap];1.00[TSI][hapmap]
rs11167705	0.88[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];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12300	0.87[CEU][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1421815	1.00[TSI][hapmap]
rs1421819	1.00[TSI][hapmap]
rs158134	0.83[ASN][1000 genomes]
rs164195	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17096232	1.00[TSI][hapmap]
rs17116409	1.00[TSI][hapmap]
rs17116411	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17116414	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17116417	1.00[TSI][hapmap]
rs17116421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17116433	1.00[CHB][hapmap]
rs17116442	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];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17116534	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs180846	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs186971	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1974776	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1974777	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2042168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2112223	1.00[CEU][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2161128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2258437	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2396999	0.93[CEU][hapmap];0.89[YRI][hapmap]
rs2431184	0.96[ASN][1000 genomes]
rs2544859	0.93[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2544860	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2544866	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2544874	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2544875	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2544876	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2544880	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]
rs2544884	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]
rs255529	0.82[ASN][1000 genomes]
rs2560063	0.95[EUR][1000 genomes]
rs2644743	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];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2644744	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2644746	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2688186	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688187	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2688188	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688189	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2688190	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2688191	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688193	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688194	0.82[EUR][1000 genomes]
rs2688195	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2688198	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2688199	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2688200	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2688201	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];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2688206	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2688208	1.00[CEU][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap];0.95[EUR][1000 genomes]
rs286623	0.81[ASN][1000 genomes]
rs286624	0.83[ASN][1000 genomes]
rs32427	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs348748	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs348749	0.86[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs348750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs348751	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs348752	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];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs348754	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3776984	1.00[TSI][hapmap]
rs39614	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];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4354100	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs454161	0.96[ASN][1000 genomes]
rs4958771	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55770418	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56374414	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58415346	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59525998	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59749917	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6580122	0.86[ASN][1000 genomes]
rs6865950	1.00[TSI][hapmap]
rs6879277	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6884416	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6895741	1.00[TSI][hapmap]
rs702742	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73276742	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73280705	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7716019	1.00[TSI][hapmap]
rs7723269	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs816717	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];0.89[EUR][1000 genomes];0.92[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];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs816720	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];0.80[YRI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs816722	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs816734	0.84[ASN][1000 genomes]
rs816743	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs816747	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs888694	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs960499	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs348739	EBF1	cis	parietal	SCAN
rs348739	ANXA6	cis	parietal	SCAN
rs348739	POMZP3	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154264000-154312800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr5:154266200-154312200	Strong transcription	Fetal Thymus	thymus
3	chr5:154266200-154316600	Weak transcription	Stomach Mucosa	stomach
4	chr5:154266400-154311200	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr5:154266400-154312800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr5:154266400-154315600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:154266600-154312800	Strong transcription	Fetal Intestine Large	intestine
8	chr5:154266600-154313200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr5:154266600-154313600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr5:154267000-154304400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr5:154267000-154312800	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr5:154267200-154311800	Strong transcription	Primary B cells from peripheral blood	blood
13	chr5:154267200-154312800	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr5:154267600-154301600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr5:154267600-154313200	Strong transcription	Duodenum Mucosa	Duodenum
16	chr5:154267800-154315600	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr5:154268000-154315600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:154268200-154315000	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr5:154268200-154315600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr5:154268200-154316200	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr5:154268800-154312800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr5:154269800-154313600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr5:154269800-154315400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr5:154269800-154316200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr5:154273600-154316600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr5:154275400-154313400	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr5:154276200-154314600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr5:154279000-154304400	Strong transcription	Fetal Muscle Trunk	muscle
29	chr5:154279400-154312200	Strong transcription	Liver	Liver
30	chr5:154280200-154311400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr5:154283200-154316600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr5:154283600-154301600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr5:154284600-154305400	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr5:154286000-154304000	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr5:154286000-154312000	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr5:154290000-154301000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr5:154290800-154311800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr5:154291200-154303200	Weak transcription	Colonic Mucosa	Colon
39	chr5:154291400-154302400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr5:154291400-154302600	Weak transcription	Brain Angular Gyrus	brain
41	chr5:154291400-154305400	Weak transcription	Esophagus	oesophagus
42	chr5:154291400-154306000	Weak transcription	Pancreas	Pancrea
43	chr5:154291600-154316600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr5:154292600-154306000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr5:154292600-154316200	Weak transcription	Fetal Heart	heart
46	chr5:154292800-154302600	Weak transcription	Rectal Smooth Muscle	rectum
47	chr5:154292800-154305400	Weak transcription	Gastric	stomach
48	chr5:154292800-154306000	Weak transcription	Right Ventricle	heart
49	chr5:154293000-154303000	Weak transcription	Brain Substantia Nigra	brain
50	chr5:154293000-154304000	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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