Variant report

Variant	rs3777434
Chromosome Location	chr6:131188312-131188313
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NRF1	chr6:131188288-131188466	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
EPB41L2	TF binding region

Extended variants
information (count: 71 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs11754472	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12193574	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs12526896	0.82[JPT][hapmap]
rs12530288	0.82[JPT][hapmap]
rs13437326	0.88[CEU][hapmap]
rs17180687	0.88[CEU][hapmap]
rs17770255	0.96[CEU][hapmap]
rs17784418	0.88[CEU][hapmap]
rs17785507	0.88[CEU][hapmap]
rs2005012	0.88[ASN][1000 genomes]
rs2068147	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs2183967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28482889	0.88[CEU][hapmap]
rs3734186	0.82[CHD][hapmap]
rs3777435	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777436	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777440	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs3777441	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs3777442	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs3777455	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs3777458	0.91[JPT][hapmap]
rs3777461	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs3777466	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs3798249	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs3798250	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs3822863	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs4075264	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4357159	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs4895901	0.87[CEU][hapmap]
rs4895903	0.90[CEU][hapmap]
rs4895907	0.88[CEU][hapmap]
rs4895908	0.88[CEU][hapmap]
rs4897468	0.96[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4897469	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4897471	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs4897472	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs4897473	0.96[CEU][hapmap];0.86[TSI][hapmap]
rs4897484	0.88[CEU][hapmap]
rs4897485	0.86[CEU][hapmap]
rs59946987	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6569707	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6569708	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6569710	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6900737	0.87[YRI][hapmap]
rs6906478	0.88[CEU][hapmap]
rs6919007	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6926250	0.83[CEU][hapmap]
rs6928920	0.82[CEU][hapmap]
rs6931804	0.92[CEU][hapmap]
rs6935108	0.91[CEU][hapmap]
rs6936553	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6941712	0.82[JPT][hapmap]
rs7739379	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7756353	0.87[YRI][hapmap]
rs7760965	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7761415	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7770860	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7775013	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.91[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];0.99[ASN][1000 genomes]
rs872576	0.96[CEU][hapmap]
rs872577	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9321260	0.81[JPT][hapmap]
rs933063	0.91[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs9385564	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9388855	0.82[CHD][hapmap]
rs9388861	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9388863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9402292	0.92[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9402299	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs942	0.85[CEU][hapmap]
rs9492755	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs954211	0.88[CEU][hapmap]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3777434	ARG1	cis	cerebellum	SCAN
rs3777434	EPB41L2	cis	parietal	SCAN
rs3777434	EPB41L2	cis	lymphoblastoid	seeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131149400-131213200	Weak transcription	Pancreas	Pancrea
2	chr6:131151600-131216600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr6:131158200-131190600	Weak transcription	Spleen	Spleen
4	chr6:131158200-131214400	Weak transcription	Lung	lung
5	chr6:131159000-131229000	Weak transcription	Colonic Mucosa	Colon
6	chr6:131168400-131190600	Weak transcription	Duodenum Mucosa	Duodenum
7	chr6:131168800-131214600	Weak transcription	Fetal Kidney	kidney
8	chr6:131170000-131189000	Strong transcription	Adipose Nuclei	Adipose
9	chr6:131170400-131193000	Weak transcription	Fetal Thymus	thymus
10	chr6:131170400-131217400	Weak transcription	Psoas Muscle	Psoas
11	chr6:131170600-131190400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:131170600-131192600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr6:131170600-131193000	Weak transcription	Primary T cells from cord blood	blood
14	chr6:131170600-131213800	Weak transcription	GM12878-XiMat	blood
15	chr6:131170800-131189000	Strong transcription	Fetal Muscle Trunk	muscle
16	chr6:131171200-131209600	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr6:131171200-131223200	Weak transcription	Right Ventricle	heart
18	chr6:131171400-131220200	Weak transcription	Fetal Brain Male	brain
19	chr6:131172800-131189400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr6:131173000-131207000	Weak transcription	Brain Substantia Nigra	brain
21	chr6:131173400-131190800	Weak transcription	Esophagus	oesophagus
22	chr6:131175000-131222400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr6:131175200-131190600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr6:131175200-131190600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr6:131175200-131214000	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr6:131175400-131194200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr6:131175400-131203600	Weak transcription	A549	lung
28	chr6:131175400-131211200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr6:131175600-131190400	Weak transcription	Colon Smooth Muscle	Colon
30	chr6:131175600-131190600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr6:131175600-131205400	Weak transcription	NH-A	brain
32	chr6:131175600-131221600	Weak transcription	Rectal Smooth Muscle	rectum
33	chr6:131176200-131190800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr6:131176800-131188400	Strong transcription	Fetal Lung	lung
35	chr6:131177200-131209200	Weak transcription	HUVEC	blood vessel
36	chr6:131179200-131214000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr6:131179400-131222400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr6:131179600-131210600	Weak transcription	NHEK	skin
39	chr6:131179600-131215000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr6:131180000-131203200	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr6:131180800-131191600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr6:131181200-131188800	Strong transcription	Fetal Muscle Leg	muscle
43	chr6:131181400-131193800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr6:131181400-131214400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:131181800-131188600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr6:131182000-131188800	Strong transcription	Placenta	Placenta
47	chr6:131182600-131189000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr6:131182600-131191600	Strong transcription	Dnd41	blood
49	chr6:131183000-131189400	Strong transcription	Left Ventricle	heart
50	chr6:131183000-131192400	Weak transcription	Small Intestine	intestine

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