Variant report

Variant	rs1974776
Chromosome Location	chr5:154291496-154291497
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 98 )
Associated
traits (count: 2 )

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];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];0.89[YRI][hapmap];0.81[EUR][1000 genomes];0.85[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];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1421813	0.80[AMR][1000 genomes]
rs1421815	1.00[TSI][hapmap]
rs1421819	1.00[TSI][hapmap]
rs158134	0.83[ASN][1000 genomes]
rs164195	0.82[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	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];0.81[EUR][1000 genomes];0.85[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];0.91[EUR][1000 genomes];0.92[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];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs180846	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs186971	0.87[AMR][1000 genomes];0.95[EUR][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];1.00[AFR][1000 genomes];1.00[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];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2112223	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2161128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2396999	0.93[CEU][hapmap]
rs2431184	0.96[ASN][1000 genomes]
rs2544859	0.93[CEU][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2544860	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2544866	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2544874	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2544875	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2544876	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2544880	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]
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];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs255529	0.82[ASN][1000 genomes]
rs2560063	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[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];1.00[EUR][1000 genomes];1.00[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];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2644746	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2688186	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688187	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2688188	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688189	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2688190	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2688191	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688193	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688194	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2688195	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[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];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2688199	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2688200	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[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];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2688206	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2688208	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];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]
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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs348748	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs348749	0.86[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs348751	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs348754	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4354100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs454161	0.96[ASN][1000 genomes]
rs4958771	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55770418	0.81[AFR][1000 genomes];0.89[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];0.80[AMR][1000 genomes]
rs6879277	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6884416	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[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];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73276742	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73280705	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7709899	0.80[AMR][1000 genomes]
rs7716019	1.00[TSI][hapmap]
rs7723269	0.81[EUR][1000 genomes];0.85[ASN][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];0.89[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];0.87[EUR][1000 genomes];0.92[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];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs816722	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs816734	0.84[ASN][1000 genomes]
rs816743	0.94[AFR][1000 genomes];1.00[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[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs960499	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1974776	ANXA6	cis	parietal	SCAN
rs1974776	EBF1	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154262800-154300800	Strong transcription	Fetal Brain Female	brain
2	chr5:154264000-154312800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr5:154266200-154312200	Strong transcription	Fetal Thymus	thymus
4	chr5:154266200-154316600	Weak transcription	Stomach Mucosa	stomach
5	chr5:154266400-154293600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr5:154266400-154311200	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr5:154266400-154312800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr5:154266400-154315600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr5:154266600-154292600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr5:154266600-154292800	Strong transcription	Left Ventricle	heart
11	chr5:154266600-154293000	Strong transcription	Dnd41	blood
12	chr5:154266600-154293200	Strong transcription	Placenta	Placenta
13	chr5:154266600-154294600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr5:154266600-154312800	Strong transcription	Fetal Intestine Large	intestine
15	chr5:154266600-154313200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr5:154266600-154313600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr5:154266800-154293000	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr5:154266800-154293600	Strong transcription	Stomach Smooth Muscle	stomach
19	chr5:154267000-154293600	Strong transcription	Primary T cells from cord blood	blood
20	chr5:154267000-154294400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr5:154267000-154304400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr5:154267000-154312800	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr5:154267200-154293000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr5:154267200-154311800	Strong transcription	Primary B cells from peripheral blood	blood
25	chr5:154267200-154312800	Strong transcription	H1 Cell Line	embryonic stem cell
26	chr5:154267400-154299000	Strong transcription	Fetal Stomach	stomach
27	chr5:154267600-154300000	Strong transcription	Fetal Muscle Leg	muscle
28	chr5:154267600-154301600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr5:154267600-154313200	Strong transcription	Duodenum Mucosa	Duodenum
30	chr5:154267800-154315600	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr5:154268000-154296600	Weak transcription	Right Atrium	heart
32	chr5:154268000-154315600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr5:154268200-154300200	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr5:154268200-154315000	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr5:154268200-154315600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr5:154268200-154316200	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr5:154268800-154312800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr5:154269600-154293200	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr5:154269800-154292200	Weak transcription	Fetal Heart	heart
40	chr5:154269800-154313600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr5:154269800-154315400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr5:154269800-154316200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr5:154273600-154316600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr5:154275000-154293000	Strong transcription	Osteobl	bone
45	chr5:154275000-154300800	Strong transcription	Primary B cells from cord blood	blood
46	chr5:154275400-154313400	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr5:154276200-154314600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr5:154277800-154293000	Strong transcription	Brain Inferior Temporal Lobe	brain
49	chr5:154279000-154304400	Strong transcription	Fetal Muscle Trunk	muscle
50	chr5:154279400-154312200	Strong transcription	Liver	Liver

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