Variant report

Variant	rs3742062
Chromosome Location	chr12:51128832-51128833
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51128569..51131031-chr12:51157006..51160452,4	MCF-7	breast:
2	chr12:51127689..51130073-chr12:51139077..51141310,3	K562	blood:
3	chr12:50898273..50899102-chr12:51128158..51129050,3	MCF-7	breast:
4	chr12:51127859..51130174-chr12:51157810..51160404,2	K562	blood:
5	chr12:50898202..50899146-chr12:51127703..51129153,4	K562	blood:
6	chr12:51128503..51131491-chr12:51131900..51134268,2	K562	blood:

Variant related genes	Relation type
ENSG00000066084	Chromatin interaction
ENSG00000123268	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1047912	0.92[CEU][hapmap]
rs10747583	0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes]
rs10783387	0.95[CHB][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap];0.82[YRI][hapmap]
rs10876045	0.85[AMR][1000 genomes]
rs10876055	0.92[CEU][hapmap];0.89[CHB][hapmap];0.84[YRI][hapmap];0.88[AMR][1000 genomes]
rs10876059	0.88[AMR][1000 genomes]
rs10876066	0.88[AMR][1000 genomes]
rs10876074	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10876084	0.94[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs10876087	0.82[ASN][1000 genomes]
rs10876098	0.95[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap]
rs11169453	0.83[AMR][1000 genomes]
rs11169484	0.92[CEU][hapmap];0.89[CHB][hapmap];0.88[AMR][1000 genomes]
rs11169486	0.88[AMR][1000 genomes]
rs11169490	0.86[AMR][1000 genomes]
rs11169492	0.88[AMR][1000 genomes]
rs11169506	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11169520	0.87[CEU][hapmap]
rs11169523	0.92[CEU][hapmap];0.89[CHB][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11169524	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[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];0.81[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap]
rs1129406	0.89[CHB][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap]
rs11503907	0.87[ASN][1000 genomes]
rs12307178	0.88[AMR][1000 genomes]
rs12372538	0.84[AMR][1000 genomes]
rs12372718	0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.82[ASN][1000 genomes]
rs12425362	0.83[AMR][1000 genomes]
rs12427378	0.88[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12582683	0.81[AMR][1000 genomes]
rs12814717	0.88[AMR][1000 genomes]
rs12818741	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12825915	0.84[AMR][1000 genomes]
rs1316442	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1316607	1.00[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.87[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13378012	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1967576	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2090852	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2139930	0.88[ASW][hapmap];0.92[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];0.93[MKK][hapmap];0.91[TSI][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2264734	0.93[ASN][1000 genomes]
rs2280503	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]
rs2684908	0.84[CHB][hapmap]
rs2700478	0.86[ASN][1000 genomes]
rs34553264	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[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];0.95[MKK][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes]
rs4388959	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4768903	0.84[CEU][hapmap]
rs4986838	0.88[CHB][hapmap]
rs61699126	0.85[AMR][1000 genomes]
rs61926278	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6580761	0.84[CHB][hapmap]
rs7133160	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7133687	0.84[AMR][1000 genomes]
rs7133974	0.95[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap]
rs7137845	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7298661	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs7298665	0.92[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7302435	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][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];0.87[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes]
rs7955736	0.88[CEU][hapmap]
rs7965652	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs876080	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9788075	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9943712	0.82[ASN][1000 genomes]

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs3742062	KIAA1463	cis	multi-tissue	Pritchard
rs3742062	KRT73	cis	parietal	SCAN
rs3742062	DIP2B	cis	multi-tissue	Pritchard
rs3742062	SLC38A1	cis	parietal	SCAN
rs3742062	DIP2B	Cis_1M	lymphoblastoid	RTeQTL
rs3742062	LASS5	cis	parietal	SCAN
rs3742062	ATF1	cis	Artery Tibial	GTEx
rs3742062	CELA1	cis	parietal	SCAN
rs3742062	LASS5	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51063200-51138600	Strong transcription	Primary monocytes fromperipheralblood	blood
2	chr12:51063600-51138800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr12:51063600-51145400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr12:51067400-51143600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr12:51067600-51142200	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr12:51068200-51141200	Strong transcription	Placenta	Placenta
7	chr12:51068200-51144000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:51074600-51139600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr12:51080200-51145400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr12:51086200-51140800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:51086200-51142600	Strong transcription	Primary T helper cells PMA-I stimulated	--
12	chr12:51090400-51145400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr12:51090600-51138400	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr12:51096000-51142000	Strong transcription	Fetal Muscle Leg	muscle
15	chr12:51096200-51144600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr12:51101000-51144800	Strong transcription	Fetal Stomach	stomach
17	chr12:51105400-51133600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr12:51108200-51142200	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr12:51110600-51141200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr12:51110600-51144800	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr12:51110800-51142200	Strong transcription	Lung	lung
22	chr12:51111400-51141600	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr12:51111400-51141800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr12:51111400-51144600	Strong transcription	Fetal Muscle Trunk	muscle
25	chr12:51111600-51142200	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr12:51111800-51136600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr12:51112000-51141800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr12:51112000-51142000	Strong transcription	Dnd41	blood
29	chr12:51112000-51144800	Strong transcription	Primary T cells from cord blood	blood
30	chr12:51112200-51144800	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr12:51114200-51144800	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr12:51114800-51129000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr12:51114800-51141800	Strong transcription	HepG2	liver
34	chr12:51114800-51142400	Strong transcription	Duodenum Mucosa	Duodenum
35	chr12:51116200-51140200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr12:51116200-51144000	Strong transcription	Fetal Intestine Large	intestine
37	chr12:51116800-51144000	Strong transcription	Primary B cells from peripheral blood	blood
38	chr12:51116800-51144800	Strong transcription	Primary B cells from cord blood	blood
39	chr12:51117200-51131200	Strong transcription	Primary hematopoietic stem cells	blood
40	chr12:51118200-51143600	Strong transcription	Adipose Nuclei	Adipose
41	chr12:51118800-51133400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr12:51119000-51139000	Strong transcription	Brain Substantia Nigra	brain
43	chr12:51119200-51130800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr12:51119200-51144600	Strong transcription	Liver	Liver
45	chr12:51120200-51140400	Strong transcription	Fetal Intestine Small	intestine
46	chr12:51120800-51139000	Strong transcription	Colonic Mucosa	Colon
47	chr12:51120800-51145400	Strong transcription	Fetal Thymus	thymus
48	chr12:51121000-51139000	Strong transcription	Spleen	Spleen
49	chr12:51121000-51140200	Strong transcription	Left Ventricle	heart
50	chr12:51121400-51130200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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