Variant report

Variant	rs2280503
Chromosome Location	chr12:51138687-51138688
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51137579..51140558-chr12:51140952..51144654,5	K562	blood:
2	chr12:51132615..51134181-chr12:51138465..51141372,2	K562	blood:
3	chr12:51137634..51140155-chr12:51140406..51142062,2	MCF-7	breast:
4	chr12:51138457..51146051-chr12:51156159..51159814,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123268	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1047912	0.92[CEU][hapmap]
rs10747583	0.91[CEU][hapmap];0.88[CHB][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes]
rs10783387	0.81[ASW][hapmap];0.95[CHB][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap];0.81[ASN][1000 genomes]
rs10876045	0.81[AMR][1000 genomes]
rs10876055	0.92[CEU][hapmap];0.89[CHB][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes]
rs10876059	0.84[AMR][1000 genomes]
rs10876066	0.84[AMR][1000 genomes]
rs10876074	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10876084	0.94[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs10876087	0.84[ASN][1000 genomes]
rs10876098	0.95[CHB][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap]
rs11169484	0.84[AMR][1000 genomes]
rs11169486	0.84[AMR][1000 genomes]
rs11169490	0.83[AMR][1000 genomes]
rs11169492	0.84[AMR][1000 genomes]
rs11169506	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11169520	0.87[CEU][hapmap]
rs11169523	0.92[CEU][hapmap];0.89[CHB][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11169524	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169567	0.95[CHB][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap]
rs11169571	0.95[CHB][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap]
rs11169578	0.89[CHB][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap]
rs1129406	0.89[CHB][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap]
rs11503907	0.89[ASN][1000 genomes]
rs12307178	0.84[AMR][1000 genomes]
rs12372538	0.80[AMR][1000 genomes]
rs12372718	0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.84[ASN][1000 genomes]
rs12427378	0.88[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12814717	0.84[AMR][1000 genomes]
rs12818741	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1316442	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1316607	1.00[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13378012	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1967576	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2090852	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2139930	0.88[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2264734	0.91[ASN][1000 genomes]
rs2684908	0.84[CHB][hapmap];0.80[CHD][hapmap]
rs2700478	0.84[ASN][1000 genomes]
rs34553264	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3742062	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3935138	0.84[CHB][hapmap]
rs3935870	1.00[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes]
rs4388959	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4768903	0.84[CEU][hapmap]
rs4986838	0.88[CHB][hapmap]
rs61699126	0.81[AMR][1000 genomes]
rs61926278	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61926303	0.81[ASN][1000 genomes]
rs6580761	0.84[CHB][hapmap]
rs7133160	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7133687	0.80[AMR][1000 genomes]
rs7133974	0.95[CHB][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap]
rs7137845	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7298661	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7298665	0.92[CEU][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7302435	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7304335	0.81[ASN][1000 genomes]
rs7306677	0.95[CHB][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap]
rs7309964	0.88[CEU][hapmap]
rs7487429	1.00[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes]
rs7955736	0.88[CEU][hapmap]
rs7965652	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7974517	0.80[AMR][1000 genomes]
rs876080	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9788075	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9943712	0.84[ASN][1000 genomes]

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2280503	ATF1	cis	Artery Tibial	GTEx
rs2280503	LASS5	cis	cerebellum	SCAN
rs2280503	SLC38A1	cis	parietal	SCAN
rs2280503	KRT73	cis	parietal	SCAN
rs2280503	DIP2B	cis	Lymphoblastoid	GTEx
rs2280503	LASS5	cis	parietal	SCAN
rs2280503	CELA1	cis	parietal	SCAN
rs2280503	DIP2B	cis	multi-tissue	Pritchard
rs2280503	KIAA1463	cis	multi-tissue	Pritchard
rs2280503	DIP2B	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51063600-51138800	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr12:51063600-51145400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr12:51067400-51143600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr12:51067600-51142200	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr12:51068200-51141200	Strong transcription	Placenta	Placenta
6	chr12:51068200-51144000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:51074600-51139600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr12:51080200-51145400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr12:51086200-51140800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr12:51086200-51142600	Strong transcription	Primary T helper cells PMA-I stimulated	--
11	chr12:51090400-51145400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr12:51096000-51142000	Strong transcription	Fetal Muscle Leg	muscle
13	chr12:51096200-51144600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr12:51101000-51144800	Strong transcription	Fetal Stomach	stomach
15	chr12:51108200-51142200	Strong transcription	Sigmoid Colon	Sigmoid Colon
16	chr12:51110600-51141200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr12:51110600-51144800	Strong transcription	Rectal Mucosa Donor 31	rectum
18	chr12:51110800-51142200	Strong transcription	Lung	lung
19	chr12:51111400-51141600	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr12:51111400-51141800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr12:51111400-51144600	Strong transcription	Fetal Muscle Trunk	muscle
22	chr12:51111600-51142200	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr12:51112000-51141800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr12:51112000-51142000	Strong transcription	Dnd41	blood
25	chr12:51112000-51144800	Strong transcription	Primary T cells from cord blood	blood
26	chr12:51112200-51144800	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr12:51114200-51144800	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr12:51114800-51141800	Strong transcription	HepG2	liver
29	chr12:51114800-51142400	Strong transcription	Duodenum Mucosa	Duodenum
30	chr12:51116200-51140200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr12:51116200-51144000	Strong transcription	Fetal Intestine Large	intestine
32	chr12:51116800-51144000	Strong transcription	Primary B cells from peripheral blood	blood
33	chr12:51116800-51144800	Strong transcription	Primary B cells from cord blood	blood
34	chr12:51118200-51143600	Strong transcription	Adipose Nuclei	Adipose
35	chr12:51119000-51139000	Strong transcription	Brain Substantia Nigra	brain
36	chr12:51119200-51144600	Strong transcription	Liver	Liver
37	chr12:51120200-51140400	Strong transcription	Fetal Intestine Small	intestine
38	chr12:51120800-51139000	Strong transcription	Colonic Mucosa	Colon
39	chr12:51120800-51145400	Strong transcription	Fetal Thymus	thymus
40	chr12:51121000-51139000	Strong transcription	Spleen	Spleen
41	chr12:51121000-51140200	Strong transcription	Left Ventricle	heart
42	chr12:51121400-51142200	Strong transcription	GM12878-XiMat	blood
43	chr12:51121400-51145400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr12:51121600-51142000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:51121600-51142400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr12:51122000-51139800	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr12:51123000-51142400	Strong transcription	Skeletal Muscle Male	skeletal muscle
48	chr12:51123200-51141800	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr12:51126400-51139800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr12:51126600-51145400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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