Variant report

Variant	rs7631671
Chromosome Location	chr3:150292771-150292772
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:150291427..150293718-chr3:150321291..150323523,2	MCF-7	breast:
2	chr3:150290177..150291697-chr3:150292047..150294562,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144895	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1133494	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12695957	0.84[AFR][1000 genomes]
rs13071114	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs14434	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16862785	0.84[YRI][hapmap]
rs1818788	0.89[ASN][1000 genomes]
rs1915942	0.89[ASN][1000 genomes]
rs1915943	0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2049229	0.90[CHB][hapmap];0.82[JPT][hapmap];1.00[ASN][1000 genomes]
rs2090916	1.00[ASW][hapmap];0.86[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2204113	0.82[JPT][hapmap]
rs2868946	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2868947	1.00[ASN][1000 genomes]
rs6440683	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440684	0.84[ASN][1000 genomes]
rs6440685	0.93[ASW][hapmap];0.86[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6440688	0.80[LWK][hapmap];0.96[YRI][hapmap]
rs6764672	0.95[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6790726	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7374917	1.00[ASN][1000 genomes]
rs7628889	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638500	0.90[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7642917	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8052	1.00[ASW][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9289818	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9289820	0.84[ASN][1000 genomes]
rs9289821	0.89[ASN][1000 genomes]
rs954068	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs9809820	0.81[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9819287	0.89[ASN][1000 genomes]
rs9820529	0.81[ASN][1000 genomes]
rs9836797	0.85[ASN][1000 genomes]
rs9865177	0.89[ASN][1000 genomes]
rs9871517	0.97[AFR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532662	chr3:150180747-150633414	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7631671	EIF2A	cis	Frontal Cortex	GTEx
rs7631671	EIF2A	cis	Nerve Tibial	GTEx
rs7631671	ENSG00000144895	cis	multi-tissue	Pritchard
rs7631671	EIF2A	cis	Esophagus Muscularis	GTEx
rs7631671	EIF2A	cis	lung	GTEx
rs7631671	EIF2A	cis	normal skin	skin_eQTL
rs7631671	EIF2A	cis	multi-tissue	Pritchard
rs7631671	EIF2A	cis	Artery Tibial	GTEx
rs7631671	EIF2A	cis	Thyroid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150265200-150299400	Weak transcription	Esophagus	oesophagus
2	chr3:150265200-150302800	Weak transcription	Gastric	stomach
3	chr3:150265400-150305800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:150265600-150293400	Weak transcription	Aorta	Aorta
5	chr3:150265600-150294000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:150265600-150304200	Weak transcription	Fetal Brain Male	brain
7	chr3:150265600-150320600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:150265600-150320600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:150266000-150304600	Weak transcription	Fetal Heart	heart
10	chr3:150266000-150307600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:150266400-150293400	Weak transcription	Psoas Muscle	Psoas
12	chr3:150266400-150302200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr3:150268600-150304000	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr3:150272400-150293800	Weak transcription	Small Intestine	intestine
15	chr3:150274000-150293400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:150274000-150293600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:150274000-150303000	Weak transcription	Pancreas	Pancrea
18	chr3:150274200-150293600	Weak transcription	Brain Substantia Nigra	brain
19	chr3:150274400-150293400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:150274800-150300600	Weak transcription	Stomach Mucosa	stomach
21	chr3:150277200-150305200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr3:150277400-150293800	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr3:150278000-150306800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:150278200-150304800	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr3:150278400-150306400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:150279400-150303800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:150280000-150304800	Strong transcription	Fetal Thymus	thymus
28	chr3:150280200-150304400	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr3:150280200-150304600	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr3:150280200-150304800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr3:150280200-150305000	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr3:150280200-150307800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:150280800-150300400	Strong transcription	Liver	Liver
34	chr3:150281400-150303800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr3:150282400-150295600	Strong transcription	Placenta	Placenta
36	chr3:150283200-150305200	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr3:150283400-150293600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:150284200-150293800	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr3:150285400-150293600	Weak transcription	Right Ventricle	heart
40	chr3:150285600-150293600	Weak transcription	Brain Angular Gyrus	brain
41	chr3:150286600-150293200	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr3:150286600-150293600	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr3:150286600-150293600	Weak transcription	NHLF	lung
44	chr3:150286600-150294400	Weak transcription	K562	blood
45	chr3:150286600-150305400	Weak transcription	Colonic Mucosa	Colon
46	chr3:150286800-150293400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr3:150286800-150293600	Weak transcription	Ovary	ovary
48	chr3:150287400-150293600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr3:150287600-150294400	Weak transcription	Fetal Kidney	kidney
50	chr3:150288000-150293200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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